Contacts of the helix formed by residues 82 - 88 (chain D) in PDB entry 4G7Z
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 LYS 82 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1115C LEU* 4.8 21.4 - - + +
55D ASP* 3.0 16.6 - - - +
56D TYR* 3.4 33.7 - - + +
81D THR* 1.3 81.4 - - + +
83D SER* 1.3 63.7 + - - +
84D ILE* 2.9 19.2 + - + +
85D VAL* 3.1 20.1 + - - +
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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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52D PRO* 3.6 12.8 - - - -
53D ILE 3.2 27.3 + - - -
55D ASP* 2.7 27.8 + - - +
81D THR 3.2 4.6 + - - -
82D LYS* 1.3 71.5 - - - +
84D ILE* 1.3 60.2 + - - +
85D VAL* 2.9 8.7 + - - +
86D ARG* 3.0 25.3 + - - +
523D ASP* 4.3 5.4 + - - +
337F HIS* 2.9 23.5 + - - -
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Residues in contact with ILE 84 (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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1060C ILE* 5.6 3.6 - - + -
1083C GLU* 5.6 0.2 - - - +
1115C LEU* 3.5 26.7 - - + -
55D ASP* 4.5 0.8 + - - +
82D LYS* 2.9 14.7 + - + +
83D SER* 1.3 80.7 + - - +
85D VAL* 1.3 63.0 + - - +
86D ARG 3.0 2.5 - - - -
87D ARG* 3.1 45.3 + - + +
88D TYR* 3.7 24.2 - - + +
523D ASP* 5.2 1.8 - - - +
337F HIS* 5.9 2.2 - - + -
338F LEU* 3.5 32.5 - - + -
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Residues in contact with VAL 85 (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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1115C LEU* 3.5 36.1 - - + -
50D PHE 3.5 17.4 - - - +
51D GLY* 3.9 13.7 - - - -
52D PRO* 4.0 8.7 - - + -
81D THR* 4.8 9.9 - - + +
82D LYS 3.1 18.4 + - - +
83D SER 2.9 3.4 + - - +
84D ILE* 1.3 77.4 - - - +
86D ARG* 1.3 59.2 + - - +
87D ARG 3.0 0.9 - - - -
88D TYR* 2.9 22.3 + - - -
89D ARG* 2.9 47.2 + - + +
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Residues in contact with ARG 86 (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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39D PRO* 4.3 6.1 - - - +
45D PHE* 3.6 19.6 - - - +
46D ASP 3.2 40.2 + - - +
47D GLU* 4.2 1.4 - - - +
50D PHE* 4.0 5.6 - - - -
51D GLY 3.4 26.3 + - - +
52D PRO 3.9 17.3 - - - +
53D ILE* 4.0 27.4 - - - +
83D SER* 3.0 13.5 + - - +
85D VAL* 1.3 78.3 - - - +
87D ARG* 1.3 55.1 + - - +
88D TYR 3.2 0.2 - - - -
521D PRO* 3.1 17.5 - - - +
522D PRO* 3.2 36.7 + - + +
523D ASP* 3.2 44.5 + - - +
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Residues in contact with ARG 87 (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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1015C LEU 3.5 7.2 + - - -
1016C ILE* 2.5 27.8 + - - -
1018C GLN* 3.2 35.6 - - - +
1083C GLU* 3.6 26.5 + - - +
1086C ARG 5.5 0.2 - - - +
1087C VAL* 3.3 18.8 - - - +
1090C LYS* 4.1 2.6 - - - +
84D ILE* 3.4 34.5 - - + +
85D VAL 3.0 1.2 - - - -
86D ARG* 1.3 75.8 - - - +
88D TYR* 1.3 71.7 + - + +
521D PRO* 3.3 19.1 - - - +
523D ASP* 3.4 30.5 + - + +
524D LEU* 3.6 26.9 - - + +
338F LEU* 4.4 5.6 - - - +
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Residues in contact with TYR 88 (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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1083C GLU* 2.7 40.4 + - - -
1086C ARG* 3.6 21.3 + - + -
1090C LYS* 3.0 29.7 - - + -
1112C PHE* 3.7 33.7 - + + -
1115C LEU* 4.0 25.4 - - + -
1116C ALA* 3.9 18.8 - - + +
84D ILE* 3.7 38.0 - - + +
85D VAL* 2.9 8.5 + - - +
86D ARG 3.2 0.6 - - - -
87D ARG* 1.3 95.0 - - + +
89D ARG* 1.3 66.9 + - - +
521D PRO* 3.3 5.5 - - - +
524D LEU* 6.2 0.2 - - + -
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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