Contacts of the helix formed by residues 514 - 535 (chain A) in PDB entry 3HR4
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO 514 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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512A GLU 3.7 8.4 - - - +
513A ILE* 1.3 91.6 - - + +
515A LEU* 1.3 66.1 + - - +
516A LYS* 4.1 10.8 - - + -
517A VAL* 2.9 35.6 + - + +
518A LEU* 3.2 9.5 + - - +
14B GLU* 4.0 13.5 - - - +
124B MET* 5.1 1.3 - - + -
127B GLU* 3.5 18.2 - - - +
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Residues in contact with LEU 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A ILE 3.4 3.0 + - - -
514A PRO* 1.3 68.9 - - - +
516A LYS* 1.3 62.1 - - - +
517A VAL 3.0 0.2 + - - -
518A LEU* 3.2 15.6 + - + -
519A VAL* 2.9 35.9 + - + +
92B PHE* 5.1 5.6 - - + -
100B ILE* 6.3 2.0 - - + -
105B LEU* 3.8 36.1 - - + -
124B MET* 3.4 32.1 - - + +
125B ILE* 5.5 0.9 - - - -
127B GLU* 2.7 17.9 + - + +
128B ALA* 5.7 1.1 - - + -
136B VAL* 5.9 4.9 - - + -
141B PHE* 5.3 0.9 - - + -
144B MET* 3.2 35.2 - - + -
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Residues in contact with LYS 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514A PRO* 4.1 11.0 - - + -
515A LEU* 1.3 73.2 - - - +
517A VAL* 1.3 62.2 + - - +
519A VAL* 4.0 4.1 - - - +
520A LYS* 3.5 28.8 + - - +
7B GLU* 3.5 16.1 + - - +
11B GLU* 2.8 40.9 + - - +
127B GLU* 2.9 24.1 + - + +
144B MET* 3.9 30.9 - - + +
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Residues in contact with VAL 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A ILE* 3.3 16.4 - - + -
514A PRO* 2.9 31.6 + - + +
516A LYS* 1.3 78.7 - - + +
518A LEU* 1.3 69.4 + - - +
519A VAL 3.1 1.1 - - - -
520A LYS* 2.9 19.0 + - - +
521A ALA 3.1 8.3 + - - -
11B GLU* 3.9 27.6 - - + +
14B GLU* 3.6 24.2 - - + +
15B ALA* 3.7 30.0 - - - +
18B LEU* 4.9 0.9 - - + -
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Residues in contact with LEU 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A ILE* 3.6 14.8 - - + +
514A PRO 3.2 8.2 + - - +
515A LEU* 3.7 21.5 - - + +
517A VAL* 1.3 77.8 - - - +
519A VAL* 1.3 58.6 + - - +
521A ALA* 2.8 21.5 + - + +
522A VAL* 2.9 19.3 + - + +
18B LEU* 3.9 18.4 - - + -
39B LEU* 5.6 2.7 - - + -
92B PHE* 3.7 31.4 - - + -
105B LEU* 5.1 1.1 - - + -
108B VAL* 4.8 2.5 - - + -
109B MET* 3.8 25.6 - - + -
112B LEU* 3.6 27.1 - - + -
124B MET* 5.6 1.3 - - - -
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Residues in contact with VAL 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515A LEU* 2.9 38.1 + - + +
516A LYS* 4.0 9.6 - - - +
518A LEU* 1.3 78.5 - - - +
520A LYS* 1.3 60.6 + - - +
522A VAL* 3.0 21.0 - - - +
523A LEU* 3.1 12.3 + - - +
92B PHE* 3.9 8.7 - - + -
141B PHE* 3.3 28.7 - - + -
144B MET* 3.7 6.7 - - + -
145B MET* 3.0 45.0 - - + +
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Residues in contact with LYS 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516A LYS* 3.5 13.5 + - - +
517A VAL 2.9 10.2 + - - +
519A VAL* 1.3 81.8 - - + +
521A ALA* 1.3 56.4 + - - +
523A LEU* 3.4 8.5 - - - +
524A PHE* 3.2 21.0 + - - +
8B GLN* 4.4 15.7 - - - +
11B GLU* 2.9 43.2 + - + +
12B PHE* 3.6 46.4 - - + +
15B ALA* 4.2 6.1 - - + -
68B PHE* 5.4 0.9 - - - -
72B MET* 3.7 9.9 - - - +
76B MET* 4.8 5.1 - - + +
144B MET 4.4 8.1 + - - -
145B MET* 3.7 26.5 + - - +
147B ALA* 5.5 4.2 - - - +
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Residues in contact with ALA 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517A VAL 3.1 9.0 + - - +
518A LEU* 2.8 12.2 + - + +
520A LYS* 1.3 74.7 - - - +
522A VAL* 1.3 58.5 + - - +
523A LEU 3.1 1.6 - - - -
524A PHE* 3.2 22.1 + - - +
525A ALA 3.2 5.7 + - - -
15B ALA* 4.0 20.1 - - + +
18B LEU* 4.1 16.2 - - + -
19B PHE* 3.3 30.7 - - + -
35B VAL* 6.2 0.9 - - + -
39B LEU* 5.4 0.4 - - - -
68B PHE* 5.4 0.4 - - - -
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Residues in contact with VAL 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518A LEU* 2.9 15.3 + - + +
519A VAL* 3.0 29.2 - - + +
521A ALA* 1.3 71.3 - - - +
523A LEU* 1.3 60.7 + - - +
524A PHE 3.1 0.4 - - - -
525A ALA* 3.8 1.2 - - - +
526A CYS* 3.0 29.0 + - - -
39B LEU* 3.8 26.2 - - + -
88B ALA* 4.3 10.1 - - + +
91B VAL* 3.8 41.3 - - + -
92B PHE* 3.8 20.6 - - + -
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Residues in contact with LEU 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519A VAL 3.1 17.9 + - - +
520A LYS* 3.4 7.0 - - - +
521A ALA 3.1 0.2 - - - -
522A VAL* 1.3 77.7 - - - +
524A PHE* 1.3 59.6 + - - +
526A CYS* 3.5 1.7 + - + -
527A MET* 3.0 37.4 + - - +
72B MET* 3.7 22.4 - - + -
76B MET* 3.8 22.0 - - - -
81B SER* 6.0 1.8 - - - -
84B GLU* 3.9 40.8 - - + +
85B ILE* 4.1 6.3 - - + +
88B ALA* 4.4 4.7 - - - -
145B MET* 3.2 27.8 - - + -
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Residues in contact with PHE 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520A LYS 3.2 12.2 + - - +
521A ALA* 3.2 10.3 - - - +
522A VAL 3.1 0.2 - - - -
523A LEU* 1.3 76.1 - - - +
525A ALA* 1.3 64.0 + - - +
527A MET* 3.3 5.6 + - - +
528A LEU* 3.3 47.9 + - + +
19B PHE* 3.5 26.9 - + + -
27B ILE* 4.8 6.1 - - + -
32B LEU* 4.1 14.4 - - + -
55B VAL* 4.5 12.8 - - + -
63B ILE* 4.5 10.8 - - + -
68B PHE* 3.5 37.0 - + + -
71B MET* 3.3 36.1 - - + -
72B MET* 3.8 17.2 - - - +
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Residues in contact with ALA 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521A ALA 3.2 7.4 + - - +
522A VAL 3.9 2.0 - - - +
523A LEU 3.4 0.2 - - - -
524A PHE* 1.3 81.3 - - - +
526A CYS* 1.3 56.5 + - - +
528A LEU* 3.0 14.9 + - - +
529A MET 2.9 24.4 + - - -
19B PHE* 4.4 7.4 - - + -
36B MET* 3.8 14.1 - - + +
39B LEU* 3.9 20.6 - - + -
41B GLN* 3.2 30.1 - - - +
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Residues in contact with CYS 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522A VAL* 3.0 25.8 + - - +
523A LEU* 3.9 4.9 - - + +
525A ALA* 1.3 76.3 - - - +
527A MET* 1.3 62.7 + - - +
529A MET* 4.2 3.1 - - - +
530A ARG* 3.1 26.7 + - - +
41B GLN* 3.7 11.0 - - - -
84B GLU* 4.3 9.0 - - - +
87B GLU* 3.7 33.9 - - + +
88B ALA* 3.8 6.5 - - - -
91B VAL* 3.6 30.7 - - - -
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Residues in contact with MET 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523A LEU* 3.0 40.9 + - + +
524A PHE* 3.6 4.9 - - - +
525A ALA 3.3 0.2 - - - -
526A CYS* 1.3 77.4 - - - +
528A LEU* 1.3 62.1 + - - +
530A ARG* 4.0 6.1 - - - +
531A LYS* 3.7 18.2 + - - +
71B MET* 3.8 21.6 - - + +
72B MET* 3.5 28.3 - - - +
75B LYS* 3.3 52.6 + - + +
76B MET 5.5 0.2 - - - -
84B GLU* 3.1 31.9 - - + +
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Residues in contact with LEU 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524A PHE* 3.3 43.5 - - + +
525A ALA* 3.0 9.7 + - - +
527A MET* 1.3 77.7 - - - +
529A MET* 1.3 63.6 + - - +
530A ARG 3.2 0.2 - - - -
531A LYS* 3.2 6.1 + - + +
532A THR* 2.9 29.6 + - - +
32B LEU* 4.0 17.3 - - + -
36B MET* 4.4 0.9 - - + -
51B MET* 3.5 35.8 - - + +
54B GLU* 4.5 11.4 - - - +
55B VAL* 4.2 11.7 - - + -
71B MET* 3.6 27.8 - - + -
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Residues in contact with MET 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525A ALA 2.9 14.0 + - - +
526A CYS* 4.2 3.8 - - - +
528A LEU* 1.3 70.0 - - - +
530A ARG* 1.3 57.2 + - - +
532A THR* 3.3 14.0 + - - -
533A MET* 2.7 65.5 + - + +
536A ARG* 4.2 8.5 - - - +
36B MET* 3.3 20.2 - - + +
41B GLN* 3.7 23.3 - - + +
42B ASN* 3.5 39.9 - - - +
43B PRO* 3.8 24.7 - - - -
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Residues in contact with ARG 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526A CYS 3.1 18.1 + - - +
527A MET 4.0 4.7 - - - +
529A MET* 1.3 75.8 - - - +
531A LYS* 1.3 57.4 + - - +
533A MET* 3.5 5.8 - - - +
534A ALA* 2.9 32.0 + - + +
75B LYS* 5.8 0.9 - - - +
80B ASP* 3.5 21.8 + - - +
83B GLU* 3.3 37.7 + - - +
84B GLU* 3.6 29.2 + - - +
87B GLU* 3.4 25.3 + - - +
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Residues in contact with LYS 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527A MET 3.7 11.1 + - - +
528A LEU* 3.2 8.2 + - - +
529A MET 3.2 0.4 - - - -
530A ARG* 1.3 79.3 - - - +
532A THR* 1.3 66.4 + - - +
534A ALA* 3.4 6.1 + - - +
535A SER* 3.2 23.1 + - - -
54B GLU* 2.9 43.9 + - - +
75B LYS* 5.4 9.0 - - - +
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Residues in contact with THR 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528A LEU 2.9 19.6 + - - +
529A MET* 3.8 15.2 + - - +
531A LYS* 1.3 75.4 - - - +
533A MET* 1.3 63.7 + - - +
535A SER* 2.7 22.0 + - - -
536A ARG* 3.2 18.4 + - - +
47B GLU* 4.0 30.9 + - - +
50B ASP* 5.3 5.4 - - + -
51B MET* 3.5 34.5 - - + -
54B GLU* 4.7 6.5 - - - +
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Residues in contact with MET 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529A MET* 2.7 42.5 + - + +
530A ARG* 3.5 6.3 - - - +
532A THR* 1.3 75.5 + - - +
534A ALA* 1.3 60.9 + - - +
535A SER 3.0 4.5 - - - -
536A ARG* 3.1 49.6 + - - +
562A SER* 5.4 5.4 - - - +
565A PHE 4.3 6.7 - - - +
566A ASN* 3.6 28.5 + - - +
567A PRO* 5.9 0.4 - - - -
42B ASN* 5.4 2.7 - - - +
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Residues in contact with ALA 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A ARG* 2.9 19.4 + - + +
531A LYS* 4.1 4.7 - - - +
533A MET* 1.3 76.4 - - - +
535A SER* 1.3 59.0 + - - +
536A ARG 3.4 4.2 - - - +
566A ASN* 4.6 8.1 + - - +
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Residues in contact with SER 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A LYS* 3.2 13.9 + - - -
532A THR* 2.7 25.5 + - - -
534A ALA* 1.3 76.2 - - - +
536A ARG* 1.3 66.3 + - - +
584A ARG* 5.6 2.1 + - - -
50B ASP* 5.7 0.7 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il