Contacts of the helix formed by residues 73 - 82 (chain D) in PDB entry 6S6A
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 GLY 73 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D ARG 3.6 0.2 - - - -
72D SER* 1.3 77.1 - - - +
74D LYS* 1.3 66.1 + - - +
75D SER 2.9 2.1 + - - -
76D SER* 3.2 9.0 + - - -
77D ILE* 3.4 25.9 + - - +
143D VAL* 4.5 0.9 - - - -
178D HIS* 4.5 0.9 - - - -
401D GDP 3.1 39.9 + - - -
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Residues in contact with LYS 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D LEU* 3.4 28.6 - - + +
67D MET* 3.6 14.6 - - - +
68D GLY 3.2 31.5 + - - +
69D LEU 3.2 17.0 + - - -
70D ARG* 4.2 4.0 - - - +
72D SER* 4.2 8.9 + - - +
73D GLY* 1.3 76.1 - - - +
75D SER* 1.3 59.3 + - - +
76D SER 3.6 0.2 - - - -
77D ILE* 4.2 0.8 - - - +
78D GLN 3.6 10.6 + - - -
114D ILE* 3.1 37.6 - - + +
115D TRP 4.0 1.6 - - - +
116D ASP* 3.2 28.7 + - - -
143D VAL* 4.8 3.3 - - + +
401D GDP 2.8 35.5 + - - +
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Residues in contact with SER 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D LYS* 1.3 72.7 - - - +
76D SER* 1.3 65.0 + - - +
78D GLN* 3.7 12.7 - - - +
79D LYS* 3.7 15.4 + - - +
114D ILE* 4.5 6.9 - - - +
401D GDP 2.2 42.4 + - - -
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Residues in contact with SER 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D GLY 3.2 0.8 + - - -
75D SER* 1.3 70.2 - - - +
77D ILE* 1.3 58.1 + - - +
79D LYS* 2.8 27.6 + - - +
80D VAL* 3.0 17.8 + - - +
220D ILE* 4.0 15.7 - - - -
401D GDP 2.6 57.7 + - - -
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Residues in contact with ILE 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D LEU* 4.9 9.4 - - + -
73D GLY 3.4 21.8 - - - +
74D LYS* 4.2 4.3 - - - +
76D SER* 1.3 76.8 - - - +
78D GLN* 1.3 64.1 + - - +
79D LYS 3.1 0.5 + - - -
80D VAL* 3.1 2.6 + - - -
81D VAL* 2.9 29.8 + - + +
112D PHE* 5.4 0.9 - - + -
143D VAL* 4.3 19.5 - - + -
176D PHE* 5.3 2.7 - - + -
178D HIS* 3.4 45.5 - - + +
220D ILE* 3.9 10.9 - - + +
225D ILE* 3.5 25.4 - - + -
229D PHE* 3.5 22.4 - - + -
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Residues in contact with GLN 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D LYS 3.6 17.1 + - - +
75D SER* 3.7 11.7 - - - +
76D SER 3.3 0.2 - - - -
77D ILE* 1.3 78.6 - - - +
79D LYS* 1.3 62.4 + - + +
82D PHE* 2.9 40.6 + - - +
83D HIS 2.4 31.5 + - - +
112D PHE* 3.7 33.6 - - + -
113D GLN* 5.6 1.0 - - - +
114D ILE* 3.9 19.3 - - + +
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Residues in contact with LYS 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D SER 3.7 9.4 + - - +
76D SER* 2.8 13.8 + - - +
78D GLN* 1.3 74.9 - - + +
80D VAL* 1.3 66.1 + - + +
81D VAL 3.5 0.2 + - - -
82D PHE 3.5 2.4 - - - -
83D HIS* 3.3 65.9 + - + +
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Residues in contact with VAL 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D SER* 3.0 16.0 + - - +
77D ILE* 3.8 7.2 - - - +
79D LYS* 1.3 78.7 - - + +
81D VAL* 1.3 60.9 + - + +
83D HIS* 4.8 5.7 + - - -
220D ILE* 4.0 45.1 - - + +
225D ILE* 4.5 6.5 - - + -
226D PHE* 3.4 33.0 - - + -
267D LYS* 4.0 6.8 + - - -
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Residues in contact with VAL 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D ILE* 2.9 19.1 + - - +
80D VAL* 1.3 79.7 - - + +
82D PHE* 1.3 87.6 + - + +
83D HIS* 5.2 0.3 - - - -
225D ILE* 3.7 29.4 - - + +
226D PHE* 3.9 13.9 - - + -
229D PHE* 3.9 19.1 - - + -
265D VAL 3.6 5.5 - - - +
266D SER* 3.2 43.0 - - - +
267D LYS* 4.4 1.7 + - - -
268D ILE* 4.2 11.4 - - + -
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Residues in contact with PHE 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D ILE* 6.2 0.9 - - + -
78D GLN* 2.9 23.8 + - - +
79D LYS 3.5 0.9 - - - -
81D VAL* 1.3 97.7 - - + +
83D HIS* 1.3 86.5 + - - +
108D SER* 3.2 34.8 - - - -
110D VAL* 4.1 13.9 - - + -
112D PHE* 3.8 51.1 - + + -
229D PHE* 3.9 13.0 - + - -
265D VAL* 4.3 21.1 - - + +
266D SER* 4.3 12.8 - - - -
268D ILE* 4.4 8.7 - - + -
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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