Contacts of the helix formed by residues 75 - 83 (chain D) in PDB entry 4Q96
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 75 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D LYS* 5.9 1.1 - - + -
74D GLY* 1.3 82.9 - - - +
76D GLU* 1.3 78.9 + - - +
77D PHE 3.4 2.0 - - - -
78D THR* 3.3 14.7 + - + +
79D ARG* 3.0 50.5 + - + +
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Residues in contact with GLU 76 (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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34D ARG* 5.0 11.5 - - + +
37D ALA* 4.5 14.1 - - + -
74D GLY* 3.3 10.1 - - - -
75D PRO* 1.3 95.8 - - - +
77D PHE* 1.3 59.2 + - + +
79D ARG* 3.4 25.7 + - - +
80D GLU* 2.9 39.0 + - + +
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Residues in contact with PHE 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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30D LEU* 3.4 31.2 - - + -
31D ILE* 4.2 2.9 - - + -
34D ARG* 3.6 23.3 - - + -
37D ALA* 3.6 26.0 - - + -
40D ILE* 3.6 34.5 - - + -
41D VAL* 4.3 3.6 - - + -
66D VAL* 3.5 31.6 - - + +
67D ILE* 4.8 2.0 - - - -
70D SER* 3.3 30.2 + - - +
74D GLY 4.6 1.4 + - - -
75D PRO 3.4 0.4 - - - -
76D GLU* 1.3 77.6 - - - +
78D THR* 1.3 62.8 + - - +
80D GLU* 4.4 0.7 - - - -
81D PHE* 2.9 46.3 + + + +
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Residues in contact with THR 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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67D ILE* 4.1 8.2 + - - +
70D SER* 4.4 2.2 + - - -
71D LYS* 3.0 44.4 + - - +
75D PRO* 3.3 16.8 + - + +
77D PHE* 1.3 78.4 - - - +
79D ARG* 1.3 59.0 + - + +
82D GLU* 3.0 33.6 + - - +
116E VAL 4.5 0.2 - - - +
117E TYR* 3.0 37.9 + - + -
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Residues in contact with ARG 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 PRO* 3.0 39.9 + - + +
76D GLU* 3.8 30.9 + - - +
78D THR* 1.3 75.0 - - + +
80D GLU* 1.3 70.2 + - + +
82D GLU* 3.3 25.8 + - - +
83D SER* 3.5 8.7 + - - -
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Residues in contact with GLU 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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37D ALA* 3.9 18.6 - - + +
38D GLY* 3.6 23.2 + - - +
41D VAL* 3.7 31.7 - - + +
76D GLU* 2.9 27.6 + - + +
77D PHE* 4.0 3.1 - - - +
79D ARG* 1.3 79.9 + - + +
81D PHE* 1.3 60.7 + - - +
83D SER* 2.9 27.2 + - - -
84D VAL 4.1 0.5 + - - -
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Residues in contact with PHE 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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30D LEU* 6.4 0.9 - - + -
40D ILE* 5.3 4.3 - - + -
41D VAL* 3.7 28.9 - - + -
44D TRP* 3.7 38.4 - + + -
62D LEU* 6.3 0.2 - - + -
63D ALA* 3.5 33.2 - - + -
66D VAL* 3.9 17.3 - - + -
67D ILE* 3.5 18.6 - - + -
77D PHE* 2.9 41.9 + + - +
80D GLU* 1.3 74.7 - - - +
82D GLU* 1.3 61.0 + - - +
84D VAL* 2.8 26.0 + - + +
85D LEU* 3.1 26.6 + - + +
117E TYR* 3.5 13.0 - - - +
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Residues in contact with GLU 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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78D THR* 3.0 22.2 + - - +
79D ARG* 3.3 17.1 + - - +
81D PHE* 1.3 76.9 - - - +
83D SER* 1.3 58.4 + - - +
84D VAL 3.4 0.9 + - - -
85D LEU* 4.1 1.7 + - - -
86D VAL* 5.1 1.0 + - - +
117E TYR* 3.6 26.9 + - + -
118E GLY 6.0 0.2 + - - -
121E PHE* 3.4 54.1 - - + +
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Residues in contact with SER 83 (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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79D ARG 3.5 7.1 + - - -
80D GLU* 2.9 19.1 + - - -
81D PHE 2.9 1.8 + - - -
82D GLU* 1.3 77.2 - - - +
84D VAL* 1.3 60.5 + - - +
87D ASP* 5.2 3.8 - - - +
207D UNX 2.7 30.4 + - - -
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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