Contacts of the strand formed by residues 84 - 89 (chain B) in PDB entry 4GKH
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 ILE 84 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A ARG* 4.7 14.4 - - + +
90A THR 5.7 1.8 - - - -
91A PRO* 3.6 21.7 - - + +
69B MSE 3.5 36.1 - - + +
72B LEU* 4.0 22.2 - - + -
73B ASN* 3.7 29.6 - - + +
82B PRO 3.9 1.5 + - - +
83B THR* 1.3 77.5 - - - +
85B LYS* 1.3 63.4 + - - +
86B HIS* 3.9 20.6 - - - +
87B PHE* 4.6 6.5 - - + +
96B LEU* 4.3 12.1 - - + -
97B LEU 3.9 3.6 - - - -
98B THR* 4.3 1.1 - - - -
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Residues in contact with LYS 85 (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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90A THR* 4.1 2.6 - - - +
91A PRO* 3.5 24.1 - - + +
22B ASP* 3.5 48.4 + - - +
26B TYR* 5.3 2.4 + - - -
50B PRO* 6.3 3.4 - - - -
52B LEU* 4.2 19.2 - - + +
83B THR* 3.3 4.2 + - + +
84B ILE* 1.3 74.6 - - - +
86B HIS* 1.3 65.1 + - - +
97B LEU* 2.8 36.2 + - + +
98B THR* 4.8 2.7 - - - +
99B THR* 4.8 12.8 - - + -
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Residues in contact with HIS 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ILE* 3.6 19.0 - - + +
89A ARG 3.4 7.9 - - - -
90A THR* 3.8 19.3 - - + +
17B SER* 3.4 26.4 + - - -
18B ASN* 3.6 14.5 + - - -
19B LEU* 3.6 26.1 + - + +
22B ASP* 2.6 24.7 + - - +
84B ILE* 3.6 4.0 - - - +
85B LYS* 1.3 79.7 - - - +
87B PHE* 1.3 72.3 + - - +
88B ILE* 3.7 23.9 - - + +
95B TRP 4.0 0.5 - - - +
96B LEU* 3.8 1.6 - - - +
97B LEU* 2.8 34.8 + - + +
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Residues in contact with PHE 87 (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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69A MSE 4.0 2.9 - - + -
87A PHE* 3.8 17.9 - + - -
88A ILE* 3.3 6.6 - - - +
89A ARG* 2.9 38.5 + - + +
65B VAL* 4.2 7.6 - - + -
66B THR* 3.5 32.1 - - - -
69B MSE 3.5 52.7 - - + -
84B ILE* 4.6 2.2 - - + -
86B HIS* 1.3 75.6 - - - +
88B ILE* 1.3 72.3 + - - +
89B ARG* 3.8 20.9 - - + -
94B ALA* 4.0 15.9 - - + -
95B TRP 3.2 23.1 - - - -
96B LEU* 3.9 11.4 - - + -
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Residues in contact with ILE 88 (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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86A HIS* 3.8 25.1 - - + +
87A PHE 3.3 4.7 - - - +
88A ILE* 4.7 8.5 - - + -
19B LEU* 3.8 40.2 - - + +
86B HIS* 3.7 16.6 - - + +
87B PHE* 1.3 84.1 - - - +
89B ARG* 1.3 62.4 + - - +
90B THR* 4.3 12.8 - - + +
93B ASP 4.0 0.3 - - - +
94B ALA* 3.3 5.2 - - - +
95B TRP* 2.9 51.7 + - + +
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Residues in contact with ARG 89 (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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69A MSE 4.7 10.7 - - - -
73A ASN* 3.5 22.9 + - - +
84A ILE* 4.9 11.2 - - + +
86A HIS* 3.3 5.5 - - - -
87A PHE* 2.8 48.6 + - + +
59B GLY 4.7 1.6 + - - -
62B ALA* 3.6 21.2 + - - +
63B ASN* 3.1 30.3 + - - +
66B THR* 3.0 27.2 + - - +
87B PHE* 3.8 16.7 - - + -
88B ILE* 1.3 75.0 - - - +
90B THR* 1.3 78.7 + - - +
91B PRO* 3.4 18.2 + - - +
93B ASP 3.2 13.6 + - - -
94B ALA* 3.7 6.3 - - - -
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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