Contacts of the strand formed by residues 61 - 69 (chain B) in PDB entry 3G4C
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 VAL 61 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A MET* 3.9 13.0 - - + +
61A VAL* 4.1 15.3 - - + -
161A THR* 4.4 2.9 - - + -
16B VAL* 3.3 6.6 - - - +
17B MET* 2.8 60.4 + - + -
58B GLU 3.9 14.4 - - - +
60B ILE* 1.3 81.7 - - - +
62B PHE* 1.3 66.8 + - - +
161B THR* 3.8 27.8 - - + -
162B VAL 3.6 11.0 - - - +
163B ASN* 4.0 6.1 - - + -
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Residues in contact with PHE 62 (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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17A MET* 4.5 0.9 - - - -
13B LEU* 4.0 9.9 - - + -
15B ASP 3.5 4.7 - - - +
16B VAL* 3.8 27.4 - - + +
60B ILE* 3.6 19.3 - - + -
61B VAL* 1.3 78.6 - - - +
63B THR* 1.3 61.9 + - - +
64B PHE* 3.4 27.8 - + + -
160B TRP 3.6 1.3 - - - +
161B THR* 3.2 5.2 - - - +
162B VAL* 2.9 37.7 + - - +
164B ALA* 4.4 7.2 - - + -
167B LEU* 3.7 22.0 - - + -
193B ILE* 4.7 0.4 - - + -
194B PHE* 3.6 37.9 - + - -
197B LYS* 4.0 17.5 - - + -
198B CYS* 3.9 14.6 - - - -
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Residues in contact with THR 63 (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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17A MET* 3.4 19.9 - - - +
59A HIS* 4.4 7.6 + - + +
13B LEU* 3.6 3.6 - - - +
14B VAL* 2.7 51.5 + - + -
15B ASP* 2.9 20.5 + - - +
62B PHE* 1.3 70.1 - - - +
64B PHE* 1.3 61.2 + - - +
159B PHE* 3.8 24.0 - - + -
160B TRP 3.2 6.3 - - - +
161B THR* 2.8 23.9 + - - +
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Residues in contact with PHE 64 (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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11B VAL* 3.7 11.4 - - + -
12B GLU 3.3 10.1 - - - +
13B LEU* 4.2 7.0 - - + -
14B VAL* 3.9 3.8 - - - -
62B PHE* 3.4 37.9 - + + -
63B THR* 1.3 78.4 - - - +
65B HIS* 1.3 58.1 + - - +
66B VAL* 4.0 16.4 - - + -
158B PHE 3.9 0.2 - - - +
159B PHE* 3.3 4.9 - - - -
160B TRP* 2.8 59.6 + + + +
162B VAL* 4.1 12.6 - - + -
167B LEU* 4.1 6.5 - - + -
190B ILE* 3.6 37.0 - - + -
193B ILE* 3.8 32.3 - - + -
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Residues in contact with HIS 65 (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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29A VAL* 4.0 7.3 + - + +
30A SER 4.7 9.6 - - - -
10B PHE* 3.7 22.3 - + - -
11B VAL* 3.6 1.0 - - - -
12B GLU* 2.7 63.2 + - - +
14B VAL* 3.7 18.8 - - + +
64B PHE* 1.3 71.2 - - - +
66B VAL* 1.3 66.6 + - - +
157B ARG* 2.9 39.3 + - + -
158B PHE 3.5 8.7 - - - -
159B PHE* 3.6 21.7 - + + -
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Residues in contact with VAL 66 (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 PHE* 3.3 11.4 - - - +
11B VAL* 4.3 8.7 - - + -
64B PHE* 4.0 20.4 - - + +
65B HIS* 1.3 79.4 - - - +
67B LYS* 1.3 62.2 + - - +
68B ALA* 4.0 4.0 - - + -
76B TRP* 3.8 26.7 - - + -
157B ARG* 3.2 5.4 - - - +
158B PHE* 2.9 69.1 + - + +
160B TRP* 5.0 0.7 - - + -
186B TYR* 3.8 21.1 - - + -
190B ILE* 5.1 0.2 - - + -
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Residues in contact with LYS 67 (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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8B LYS* 3.4 19.3 + - - +
9B GLY* 3.2 1.4 - - - -
10B PHE* 2.9 56.1 + - + +
66B VAL* 1.3 70.6 - - - +
68B ALA* 1.3 55.4 + - - +
97B GLU* 2.6 38.4 + - - -
155B TYR* 3.9 23.3 - - + -
156B THR 3.3 11.4 - - - +
157B ARG* 3.8 18.3 - - + +
186B TYR* 2.6 26.0 + - - -
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Residues in contact with ALA 68 (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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66B VAL* 4.0 11.2 + - + -
67B LYS* 1.3 77.5 - - - +
69B PRO* 1.3 80.1 - - + +
72B VAL* 4.1 12.8 - - + -
73B ALA* 4.7 1.8 - - - +
76B TRP* 5.1 0.2 - - + -
155B TYR* 3.4 6.5 - - - -
156B THR* 2.8 35.5 + - - +
158B PHE* 4.4 11.4 - - + -
186B TYR* 3.3 16.6 - - + +
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Residues in contact with PRO 69 (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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6B LEU* 4.0 12.1 - - + -
68B ALA* 1.3 90.5 - - + +
70B ILE* 1.3 67.5 + - - +
71B PHE* 3.6 29.6 - - + -
72B VAL* 2.9 16.7 + - + +
73B ALA* 2.9 19.2 + - - +
99B TYR* 3.7 22.7 - - + -
153B ASN* 4.0 12.6 - - - +
154B LEU 3.2 9.4 - - - +
155B TYR* 3.6 12.1 - - + -
186B TYR* 3.7 7.0 - - - +
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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