Contacts of the helix formed by residues 514 - 534 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512E GLU* 3.4 12.8 - - - +
513E ILE* 1.3 90.6 - - + +
515E LEU* 1.3 60.4 + - - +
516E LYS* 4.4 6.3 - - + +
517E VAL* 2.8 41.2 + - + +
518E LEU* 3.0 12.7 + - - -
14F GLU* 3.9 16.6 - - - +
124F MET* 4.6 2.5 - - + -
127F GLU* 3.6 21.1 - - - +
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Residues in contact with LEU 515 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514E PRO* 1.3 70.3 - - - +
516E LYS* 1.3 58.0 + - - +
517E VAL 3.1 0.9 - - - -
518E LEU* 4.1 15.9 - - + -
519E VAL* 3.0 48.5 + - + +
92F PHE* 4.4 3.8 - - + -
105F LEU* 4.2 26.2 - - + -
124F MET* 3.8 41.0 - - + +
125F ILE* 5.8 0.9 - - - -
127F GLU* 3.2 9.1 + - - +
128F ALA* 4.5 8.1 - - + -
136F VAL* 5.7 7.6 - - + -
141F PHE* 5.6 3.8 - - + -
144F MET* 3.2 32.8 - - + -
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Residues in contact with LYS 516 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514E PRO* 4.6 10.0 - - + +
515E LEU* 1.3 74.2 - - - +
517E VAL* 1.3 60.4 + - + +
519E VAL* 4.4 1.3 - - - -
520E LYS* 3.1 31.3 - - - +
7F GLU* 4.3 5.6 - - - +
11F GLU* 3.3 36.9 - - + +
127F GLU* 2.8 41.3 + - - +
144F MET* 3.9 34.3 - - + +
147F ALA* 5.2 11.0 - - + -
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Residues in contact with VAL 517 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513E ILE* 4.1 12.6 - - + -
514E PRO* 2.8 31.9 + - + +
516E LYS* 1.3 79.9 - - + +
518E LEU* 1.3 72.8 + - - +
519E VAL 3.1 0.9 - - - -
520E LYS* 2.7 18.0 + - - +
521E ALA 3.1 7.3 + - - -
11F GLU* 3.8 27.1 - - + +
14F GLU* 3.5 27.4 - - + +
15F ALA* 3.6 29.6 - - - +
18F LEU* 4.8 2.7 - - + -
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Residues in contact with LEU 518 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513E ILE* 4.0 8.7 - - + +
514E PRO 3.0 10.6 + - - +
515E LEU* 4.2 13.9 - - + +
517E VAL* 1.3 81.6 - - - +
519E VAL* 1.3 56.2 + - - +
521E ALA* 2.7 25.8 + - + +
522E VAL* 3.0 25.0 + - + +
18F LEU* 4.2 19.1 - - + -
92F PHE* 3.9 27.8 - - + -
105F LEU* 4.7 3.4 - - + -
108F VAL* 4.7 4.3 - - + -
109F MET* 3.7 29.6 - - - -
112F LEU* 3.7 26.9 - - + -
124F MET* 5.2 2.0 - - - -
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Residues in contact with VAL 519 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515E LEU* 3.0 47.0 + - + +
516E LYS* 4.5 2.2 - - - +
518E LEU* 1.3 79.1 - - - +
520E LYS* 1.3 67.5 + - + +
521E ALA 3.0 0.5 + - - -
522E VAL* 3.2 10.9 + - - +
523E LEU 2.9 19.1 + - - -
92F PHE* 4.0 6.7 - - + -
141F PHE* 3.8 24.9 - - + -
144F MET* 4.5 4.5 - - + -
145F MET* 3.0 51.7 - - + +
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Residues in contact with LYS 520 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516E LYS 3.1 16.6 - - - +
517E VAL 2.7 14.1 + - - +
519E VAL* 1.3 72.1 - - + +
521E ALA* 1.3 60.3 + - - +
523E LEU* 3.5 4.6 - - + +
524E PHE* 3.4 13.3 + - - +
8F GLN* 3.9 24.9 + - - +
11F GLU* 2.8 44.3 + - + +
12F PHE* 3.8 34.5 - - + -
15F ALA* 4.3 8.1 - - + +
68F PHE* 4.9 1.4 - - - -
72F MET* 3.9 9.9 - - - +
76F MET* 5.7 0.2 - - + -
144F MET 4.1 9.4 + - - -
145F MET* 3.3 42.0 + - - -
147F ALA* 4.9 3.6 - - - +
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Residues in contact with ALA 521 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517E VAL 3.1 5.2 + - - +
518E LEU* 2.7 18.4 + - + +
520E LYS* 1.3 68.3 - - - +
522E VAL* 1.3 59.1 + - + +
523E LEU 3.0 4.5 - - - -
524E PHE* 2.8 29.0 + - - +
525E ALA 3.1 4.5 + - - -
15F ALA* 4.1 11.0 - - + +
18F LEU* 3.6 28.3 - - + -
19F PHE* 3.5 27.5 - - + -
35F VAL* 6.2 0.7 - - + -
39F LEU* 5.5 0.7 - - + -
68F PHE* 5.3 0.4 - - - -
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Residues in contact with VAL 522 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518E LEU* 3.0 35.7 - - + +
519E VAL* 3.6 6.5 - - - +
521E ALA* 1.3 70.8 - - + +
523E LEU* 1.3 67.6 + - - +
525E ALA* 3.8 1.4 - - - +
526E CYS* 3.0 25.1 + - - +
39F LEU* 4.2 28.9 - - + -
88F ALA* 3.4 34.5 - - + +
91F VAL* 4.5 11.0 - - + -
92F PHE* 4.0 21.1 - - + -
108F VAL* 5.6 0.7 - - + -
141F PHE* 5.6 0.2 - - + -
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Residues in contact with LEU 523 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519E VAL 2.9 5.7 + - - -
520E LYS* 3.5 9.2 - - - +
521E ALA 3.0 0.4 - - - -
522E VAL* 1.3 76.7 - - - +
524E PHE* 1.3 65.6 + - - +
526E CYS* 3.0 4.3 + - + +
527E MET* 2.8 54.0 + - + +
72F MET* 4.0 6.5 - - + -
76F MET* 3.2 35.0 - - - -
84F GLU* 4.3 17.9 - - + -
85F ILE* 4.3 16.6 - - + +
88F ALA* 4.1 8.3 - - - -
145F MET* 3.2 35.2 - - + -
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Residues in contact with PHE 524 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520E LYS 3.4 6.1 + - - +
521E ALA 2.8 10.4 + - - +
523E LEU* 1.3 78.5 - - - +
525E ALA* 1.3 63.5 + - - +
527E MET* 3.0 16.6 + - - +
528E LEU* 3.1 35.7 + - + +
19F PHE* 3.2 37.2 - + - -
27F ILE* 4.5 5.6 - - + -
32F LEU* 4.2 7.4 - - + -
55F VAL* 4.7 5.2 - - + -
63F ILE* 4.4 20.4 - - + -
68F PHE* 3.6 36.1 - + + -
71F MET* 3.6 28.9 - - + -
72F MET* 3.7 28.4 - - - +
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Residues in contact with ALA 525 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521E ALA 3.1 6.4 + - - +
522E VAL 3.8 4.7 - - - +
524E PHE* 1.3 83.8 - - - +
526E CYS* 1.3 64.0 + - - +
528E LEU* 3.1 11.0 + - - +
529E MET 3.0 17.7 + - - -
19F PHE* 4.4 7.4 - - + -
36F MET* 3.6 18.4 - - + +
39F LEU* 3.8 23.1 - - + -
41F GLN* 3.5 22.4 - - - +
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Residues in contact with CYS 526 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522E VAL 3.0 23.0 + - - +
523E LEU* 3.0 7.0 + - + +
525E ALA* 1.3 74.1 - - - +
527E MET* 1.3 67.4 + - - +
529E MET* 3.0 1.7 + - - -
530E ARG* 2.8 21.4 + - - +
41F GLN* 3.4 13.9 - - - -
84F GLU* 4.5 3.4 - - - +
87F GLU* 3.1 33.9 - - + +
88F ALA* 3.5 28.5 - - + -
91F VAL* 3.5 19.1 - - - -
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Residues in contact with MET 527 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523E LEU* 2.8 52.7 + - + +
524E PHE* 3.2 7.6 - - - +
526E CYS* 1.3 73.5 - - - +
528E LEU* 1.3 65.0 + - + +
530E ARG* 3.3 15.5 + - - +
531E LYS* 3.3 10.9 + - - +
71F MET* 4.4 10.5 - - + +
72F MET* 3.7 22.7 - - - +
75F LYS* 3.2 58.1 - - + +
76F MET* 4.4 7.4 - - + +
81F SER* 5.1 2.2 - - - -
84F GLU* 3.2 26.5 - - + +
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Residues in contact with LEU 528 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524E PHE* 3.1 44.8 + - + +
525E ALA 3.3 6.5 - - - +
527E MET* 1.3 75.6 - - - +
529E MET* 1.3 63.3 + - - +
531E LYS* 3.2 6.5 + - + +
532E THR* 3.0 27.2 + - - +
32F LEU* 4.2 25.4 - - + -
36F MET* 4.4 2.9 - - + -
51F MET* 3.4 29.8 - - + -
54F GLU* 4.2 9.2 - - - +
55F VAL* 4.2 10.3 - - + -
71F MET* 3.3 30.5 - - + -
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Residues in contact with MET 529 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525E ALA 3.0 7.3 + - - +
526E CYS* 3.0 6.9 + - - +
528E LEU* 1.3 73.8 - - - +
530E ARG* 1.3 66.8 + - - +
532E THR* 3.6 16.6 + - - +
533E MET* 2.9 59.5 + - + +
536E ARG* 3.9 15.7 - - - +
36F MET* 3.1 31.6 - - + -
41F GLN* 3.3 35.2 - - + +
42F ASN* 4.5 9.6 - - - +
43F PRO* 4.3 14.4 - - - -
87F GLU* 4.9 2.9 - - - +
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Residues in contact with ARG 530 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526E CYS 2.8 11.2 + - - +
527E MET 3.3 11.2 - - - +
528E LEU 3.2 0.2 - - - -
529E MET* 1.3 78.6 - - - +
531E LYS* 1.3 65.7 + - + +
533E MET* 3.4 6.6 - - - +
534E ALA* 3.4 15.8 + - - +
80F ASP* 4.5 18.1 + - - +
83F GLU* 3.8 27.0 - - - +
84F GLU* 3.8 35.9 - - - +
87F GLU* 3.7 27.2 + - - +
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Residues in contact with LYS 531 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614A GLU* 3.2 27.6 + - - -
616A ASN* 4.8 14.4 - - - +
527E MET 3.3 8.3 + - - +
528E LEU* 3.2 9.6 + - + +
529E MET 3.1 0.2 - - - -
530E ARG* 1.3 75.0 - - - +
532E THR* 1.3 66.1 + - - +
533E MET 2.9 3.4 - - - -
534E ALA* 2.8 25.7 + - + +
535E SER* 3.4 6.7 + - - +
54F GLU* 3.7 33.7 + - - +
75F LYS* 5.5 11.0 - - - +
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Residues in contact with THR 532 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528E LEU 3.0 17.6 + - - +
529E MET* 3.6 22.5 + - - +
531E LYS* 1.3 74.1 - - + +
533E MET* 1.3 59.2 + - - +
535E SER* 2.9 33.8 + - - -
536E ARG* 3.6 1.6 + - - +
47F GLU* 3.5 39.5 + - - +
50F ASP* 5.1 5.4 - - + -
51F MET* 3.2 36.1 - - + -
54F GLU* 5.1 0.9 - - - +
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Residues in contact with MET 533 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529E MET* 2.9 48.2 + - + +
530E ARG* 3.4 7.6 - - - +
531E LYS 2.8 0.4 + - - -
532E THR* 1.3 73.1 + - - +
534E ALA* 1.3 54.3 + - - +
535E SER 2.6 5.1 + - - -
536E ARG* 2.6 60.0 + - - +
562E SER* 5.6 4.9 - - - +
565E PHE 3.7 14.8 - - - +
566E ASN* 3.6 36.0 + - - +
567E PRO* 5.5 2.9 - - + -
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Residues in contact with ALA 534 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A ASN* 3.6 33.8 - - - +
530E ARG 3.4 8.1 + - - +
531E LYS* 2.8 18.1 + - + +
533E MET* 1.3 72.7 - - - +
535E SER* 1.3 56.3 + - - +
536E ARG 3.3 7.3 + - - +
566E ASN* 6.1 1.1 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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