Contacts of the helix formed by residues 97 - 107 (chain B) in PDB entry 3GB9
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 THR 97 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93B LEU 3.0 18.5 + - - +
94B TRP* 4.1 5.4 + - - -
96B VAL* 1.3 77.7 - - + +
98B PHE* 1.3 66.7 + - - +
99B PRO* 3.2 3.6 - - - -
100B VAL* 2.9 20.4 + - - +
101B ARG* 3.5 12.9 + - - +
146B PRO* 3.9 5.7 + - + +
223B PRO* 3.4 46.7 - - + +
224B GLU* 3.8 5.4 - - - +
227B VAL* 3.5 25.1 - - + +
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Residues in contact with PHE 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B TYR* 3.4 41.7 - + + -
9B ASP 4.8 0.2 - - - -
10B TYR* 3.5 35.7 - + - -
13B THR* 3.6 23.1 - - - -
55B ASN* 3.9 11.0 - - + -
56B PHE* 3.5 33.4 - + - -
57B PRO* 3.8 15.3 - - + -
94B TRP 3.5 15.1 + - - +
95B LYS 3.3 11.2 + - - +
97B THR* 1.3 77.9 + - - +
99B PRO* 1.3 72.6 - - + +
100B VAL 3.2 0.3 + - - -
101B ARG* 3.3 6.7 + - - +
102B VAL* 3.2 31.4 + - + +
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Residues in contact with PRO 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ILE* 5.8 0.4 - - + -
56B PHE* 4.1 15.5 - - + -
81B MET* 3.6 42.2 - - + -
85B PHE* 4.1 10.5 - - + -
95B LYS 3.7 4.5 - - - +
96B VAL 3.3 13.0 - - - +
97B THR* 3.3 4.3 - - - -
98B PHE* 1.3 100.2 - - + +
100B VAL* 1.3 58.4 + - + +
102B VAL* 3.1 7.3 + - + +
103B PHE* 2.8 43.3 + - + -
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Residues in contact with VAL 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ILE* 4.6 12.1 - - + -
97B THR* 2.9 13.5 + - - +
99B PRO* 1.3 73.7 - - + +
101B ARG* 1.3 66.6 + - - +
103B PHE* 3.3 12.6 + - + +
104B HIS* 3.1 21.8 + - - +
111B LEU* 4.6 5.6 - - + -
224B GLU* 4.0 36.6 - - + +
227B VAL* 3.8 13.5 - - + +
228B ALA* 3.7 34.5 - - + +
231B CYS* 4.8 1.7 - - - -
233B LEU* 4.3 10.7 - - + +
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Residues in contact with ARG 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B ASN* 6.0 1.4 - - - +
10B TYR* 3.3 46.5 + - + +
97B THR* 3.5 11.6 + - - +
98B PHE* 3.3 3.8 + - - +
100B VAL* 1.3 77.1 - - - +
102B VAL* 1.3 63.2 + - - +
104B HIS* 3.3 8.3 + - - +
105B LEU* 3.3 24.5 + - - +
146B PRO 4.9 5.5 + - - -
147B LEU* 4.3 15.6 - - - +
152B ASP 6.2 0.2 - - - +
155B PHE* 3.6 42.1 - - + +
227B VAL* 3.8 26.0 - - + +
230B HIS* 3.1 35.0 + - - +
231B CYS* 3.9 8.6 - - - -
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Residues in contact with VAL 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B TYR* 4.2 11.2 - - + +
13B THR* 3.8 24.9 - - + -
14B ALA* 4.3 4.0 - - - -
17B LEU* 4.1 11.0 - - + -
56B PHE* 5.1 5.4 - - + -
98B PHE* 3.2 44.1 + - + +
99B PRO* 3.1 11.7 + - + +
101B ARG* 1.3 79.5 - - - +
103B PHE* 1.3 66.0 + - + +
105B LEU* 3.0 9.3 + - - +
106B LEU* 2.9 39.0 + - + +
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Residues in contact with PHE 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ALA* 3.4 27.1 - - + -
29B ILE 5.4 0.2 - - - -
30B ILE* 4.6 14.4 - - + -
56B PHE* 5.6 0.7 - + - -
68B LEU* 4.1 28.0 - - + -
79B VAL* 4.1 19.3 - - + -
81B MET* 4.1 21.1 - - + -
99B PRO* 2.8 41.8 + - + -
100B VAL* 3.3 14.6 + - + +
102B VAL* 1.3 75.7 - - + +
104B HIS* 1.3 62.3 + - - +
106B LEU* 3.1 29.9 + - + +
108B VAL* 3.1 34.0 + - + +
111B LEU* 4.5 6.5 - - + -
233B LEU* 5.2 4.5 - - + -
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Residues in contact with HIS 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B VAL 3.1 8.9 + - - +
101B ARG 3.5 7.6 - - - +
102B VAL 3.2 0.2 - - - -
103B PHE* 1.3 75.5 - - - +
105B LEU* 1.3 72.2 + - + +
107B GLY* 3.1 19.4 + - - -
108B VAL 4.1 10.7 + - - +
154B ARG 4.5 12.3 + - - -
155B PHE* 3.8 26.7 + + - -
231B CYS* 3.7 42.2 + - - -
233B LEU* 4.0 16.2 - - + +
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Residues in contact with LEU 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B TYR* 3.5 26.2 - - + +
10B TYR* 3.6 42.4 - - + +
11B LYS* 3.8 13.7 - - + +
14B ALA* 3.6 21.1 - - + +
18B LEU* 4.2 9.2 - - - +
101B ARG 3.3 12.0 + - - +
102B VAL* 3.0 4.2 + - - +
104B HIS* 1.3 89.8 - - + +
106B LEU* 1.3 62.7 + - - +
107B GLY 3.3 0.4 + - - -
155B PHE* 4.3 12.3 - - + -
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Residues in contact with LEU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ALA* 3.6 38.4 - - + +
17B LEU* 4.2 22.4 - - + -
18B LEU* 4.1 26.9 - - + +
24B ARG* 5.0 5.0 - - - +
25B PRO* 4.5 19.5 - - + +
70B PHE* 4.2 22.4 - - + -
79B VAL* 5.0 1.1 - - + -
102B VAL* 2.9 13.3 + - + +
103B PHE* 3.1 39.0 + - + +
105B LEU* 1.3 78.7 - - - +
107B GLY* 1.3 54.3 + - - +
108B VAL* 4.5 5.6 - - + -
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Residues in contact with GLY 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B PRO 3.9 10.0 - - - +
26B GLN* 4.8 1.9 - - - +
104B HIS 3.1 11.7 + - - -
105B LEU 3.3 1.4 + - - -
106B LEU* 1.3 79.1 - - - +
108B VAL* 1.3 67.3 + - - +
109B ASP* 3.3 6.2 + - - +
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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