Contacts of the helix formed by residues 512 - 527 (chain A) in PDB entry 1Q6X
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 ILE 512 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A THR* 3.9 28.0 - - + +
37A THR* 3.7 31.2 - - + -
38A TYR* 3.9 31.6 - - + +
41A CYS* 4.6 3.1 - - + -
463A ARG* 4.1 19.3 - - - +
502A TYR* 3.8 13.0 + - - +
505A MET* 5.2 1.1 - - + -
510A MET 4.9 2.5 - - - +
511A ALA* 1.3 84.4 - - - +
513A ASP* 1.3 78.0 + - - +
514A ASN 3.5 2.0 - - - -
515A HIS* 3.1 5.2 + - - +
516A LEU* 2.9 34.7 + - + +
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Residues in contact with ASP 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A TYR* 5.0 1.2 - - - -
460A ASP* 3.3 16.0 + - - +
461A ASN* 3.3 28.7 + - + +
463A ARG* 2.9 42.1 + - - +
502A TYR* 4.8 1.0 + - - -
511A ALA* 4.0 0.6 - - - +
512A ILE* 1.3 80.2 - - - +
514A ASN* 1.3 64.7 + - - +
516A LEU* 3.9 5.8 - - - +
517A LEU* 3.0 23.9 + - - +
543A ASN* 4.4 3.4 - - - +
545A PHE* 3.8 9.7 - - - -
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Residues in contact with ASN 514 (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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26A LEU* 5.0 3.5 - - + +
85A TRP* 3.5 19.1 - - + -
86A VAL* 3.9 24.9 - - + +
90A TRP* 3.6 25.3 - - - -
451A ILE* 4.0 12.9 - - - +
459A VAL 3.2 16.1 + - - +
460A ASP* 3.1 34.6 + - - +
512A ILE 3.5 0.6 - - - -
513A ASP* 1.3 79.7 - - - +
515A HIS* 1.3 61.7 + - - +
517A LEU* 3.2 9.9 + - - +
518A ALA 3.1 18.2 + - - -
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Residues in contact with HIS 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A VAL* 4.2 0.6 - - - +
29A PRO* 3.1 47.2 + - + +
30A PRO 4.0 2.9 - - - -
31A LEU* 4.2 4.0 - - + -
34A THR* 2.6 37.1 + - + +
72A GLN* 2.7 27.6 + - - -
75A LEU* 3.5 20.3 - - + +
85A TRP* 3.9 9.0 - + + -
511A ALA 4.4 2.8 + - - +
512A ILE 3.1 11.9 + - - +
514A ASN* 1.3 77.2 - - - +
516A LEU* 1.3 62.4 + - - +
518A ALA* 3.2 3.6 + - - +
519A LEU* 3.1 30.1 + - + +
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Residues in contact with LEU 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A THR* 3.8 21.5 - - + -
35A LEU* 4.5 5.4 - - + -
38A TYR* 3.9 31.9 - - + -
61A PHE* 5.7 0.4 - - + -
463A ARG* 6.4 0.4 - - - +
512A ILE* 2.9 31.6 + - + +
513A ASP* 3.9 5.2 - - - +
515A HIS* 1.3 75.2 - - - +
517A LEU* 1.3 64.6 + - - +
519A LEU* 3.4 16.5 + - + +
520A ARG* 3.0 26.0 + - - +
533A MET* 4.3 21.1 - - + -
534A PHE* 3.9 7.9 - - + -
539A TYR* 4.3 25.4 - - + +
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Residues in contact with LEU 517 (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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86A VAL* 4.0 13.2 - - + -
89A TYR* 4.0 8.1 - - + +
90A TRP* 3.9 37.9 - - + +
93A ASP* 3.7 21.3 - - + +
513A ASP 3.0 14.5 + - - +
514A ASN* 3.4 13.5 - - - +
515A HIS 3.2 0.2 - - - -
516A LEU* 1.3 77.6 - - - +
518A ALA* 1.3 56.6 + - - +
520A ARG* 3.2 38.4 + - - +
521A GLU* 3.0 34.1 + - + +
539A TYR* 4.7 4.9 + - - -
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Residues in contact with ALA 518 (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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75A LEU* 3.7 21.5 - - + -
85A TRP* 3.6 31.4 - - + -
86A VAL* 5.3 0.4 - - + -
89A TYR* 3.8 21.5 - - + -
514A ASN 3.1 5.7 + - - -
515A HIS 3.2 4.5 + - - +
517A LEU* 1.3 74.8 - - - +
519A LEU* 1.3 59.8 + - - +
521A GLU* 3.3 1.2 + - - +
522A LEU* 2.8 36.3 + - - +
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Residues in contact with LEU 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 3.9 24.0 - - + -
34A THR* 5.6 0.4 - - + -
35A LEU* 5.5 0.4 - - + -
61A PHE* 4.4 13.7 - - + -
68A GLY 4.6 2.0 - - - +
71A LEU* 3.5 37.3 - - + +
72A GLN* 3.9 24.5 - - - +
75A LEU* 4.2 9.6 - - + -
515A HIS* 3.1 25.4 + - + +
516A LEU* 3.8 20.6 - - + +
518A ALA* 1.3 76.6 - - - +
520A ARG* 1.3 57.9 + - - +
522A LEU* 3.3 4.0 + - + +
523A ALA* 2.9 30.1 + - - +
534A PHE* 4.0 11.2 - - + -
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Residues in contact with ARG 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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93A ASP* 2.8 29.5 + - - +
516A LEU 3.0 17.6 + - - +
517A LEU* 3.2 23.0 - - - +
519A LEU* 1.3 77.3 - - - +
521A GLU* 1.3 82.8 + - - +
523A ALA* 3.2 4.7 + - - +
524A ARG* 3.0 26.2 + - + +
531A PRO* 5.8 0.2 - - - +
534A PHE* 3.3 36.8 - - + -
539A TYR* 3.2 37.2 + - - +
543A ASN* 4.6 5.9 - - - +
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Residues in contact with GLU 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A TYR* 3.7 45.4 + - + +
93A ASP* 6.3 1.1 - - + -
517A LEU* 3.0 26.9 + - + +
518A ALA 3.3 1.3 + - - +
520A ARG* 1.3 108.5 + - - +
522A LEU* 1.3 65.2 + - - +
524A ARG* 3.1 39.6 + - - +
525A ASP* 3.3 22.5 + - - +
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Residues in contact with LEU 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LEU* 3.9 18.8 - - + +
74A LYS* 4.4 15.7 - - + +
75A LEU* 3.8 46.0 - - + +
78A ARG* 4.6 10.3 - - + +
89A TYR* 3.5 21.1 - - + +
518A ALA 2.8 22.8 + - - +
519A LEU* 3.7 7.6 - - - +
521A GLU* 1.3 75.9 - - - +
523A ALA* 1.3 61.8 + - - +
525A ASP* 3.3 5.8 + - + -
526A LEU* 3.1 38.3 + - + +
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Residues in contact with ALA 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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71A LEU* 3.8 20.1 - - + +
519A LEU 2.9 16.7 + - - +
520A ARG* 3.4 9.0 - - - +
522A LEU* 1.3 77.7 - - - +
524A ARG* 1.3 59.1 + - - +
527A CYS* 2.6 43.0 + - - +
531A PRO* 3.7 32.3 - - + +
534A PHE* 4.7 0.9 - - + -
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Residues in contact with ARG 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 ARG* 3.0 13.4 + - + +
521A GLU* 3.1 37.0 + - - +
522A LEU 3.3 0.4 - - - -
523A ALA* 1.3 77.2 - - - +
525A ASP* 1.3 64.7 + - - +
526A LEU 3.6 0.3 + - - -
527A CYS 4.1 9.4 - - - +
530A PRO* 6.5 0.7 - - - -
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Residues in contact with ASP 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A TYR* 6.1 0.9 - - - +
521A GLU 3.3 13.7 + - - +
522A LEU* 3.8 8.1 - - + +
523A ALA 3.1 0.6 - - - -
524A ARG* 1.3 85.7 + - + +
526A LEU* 1.3 72.3 + - + +
527A CYS 5.5 0.2 - - - -
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Residues in contact with LEU 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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70A THR* 6.5 0.7 - - + -
71A LEU* 4.7 9.4 - - + -
74A LYS* 4.1 36.8 - - + -
522A LEU* 3.1 26.2 + - + +
523A ALA* 3.1 3.4 + - - +
525A ASP* 1.3 99.4 - - + +
527A CYS* 1.3 65.0 + - - +
528A LYS* 4.0 6.3 + - - +
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Residues in contact with CYS 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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67A LEU* 3.8 29.2 - - - -
71A LEU* 5.1 1.8 - - - -
523A ALA* 2.6 39.4 + - - +
524A ARG* 4.1 9.9 - - - +
526A LEU* 1.3 78.1 - - - +
528A LYS* 1.3 67.1 + - - +
529A GLU* 3.2 20.5 + - - +
531A PRO* 4.4 7.2 - - + -
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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