Contacts of the strand formed by residues 92 - 98 (chain A) in PDB entry 5GKI
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 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A THR* 5.3 16.8 - - + +
17A LEU* 3.8 26.5 - - + -
86A LEU* 3.6 20.2 - - + -
87A GLU 3.6 7.2 - - - +
88A LEU* 4.5 7.6 - - + -
89A ARG 5.2 0.4 - - - +
91A ASN* 1.3 90.4 - - + +
93A VAL* 1.3 60.7 + - - +
108A GLU 3.7 0.2 - - - -
109A LEU* 2.8 43.2 + - + +
112A VAL* 5.2 1.1 - - + -
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Residues in contact with VAL 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A HIS* 6.2 0.7 - - + -
86A LEU* 3.4 7.2 - - - +
87A GLU* 2.8 38.3 + - - +
89A ARG* 3.8 35.0 - - + +
91A ASN 3.5 10.8 - - - +
92A PRO* 1.3 80.6 - - - +
94A LEU* 1.3 70.6 + - - +
95A VAL* 3.7 16.7 + - + +
106A GLU* 4.1 6.5 - - + +
107A VAL 3.1 21.1 - - - +
108A GLU* 3.9 19.3 - - + +
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Residues in contact with LEU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A VAL* 4.5 16.2 - - + -
31A LEU* 4.9 4.5 - - + -
33A ILE* 3.8 25.6 - - + -
56A ILE* 4.1 20.4 - - + -
58A VAL* 4.8 5.6 - - + -
64A PHE* 4.0 20.4 - - + -
84A VAL* 4.1 15.5 - - + -
85A ARG 3.6 11.0 - - - +
86A LEU* 4.0 15.7 - - + +
93A VAL* 1.3 72.9 - - - +
95A VAL* 1.3 58.9 + - - +
96A SER 4.2 0.4 - - - -
105A LEU 3.7 0.9 - - - +
106A GLU* 3.4 4.5 - - - -
107A VAL* 2.7 43.1 + - + +
109A LEU* 4.1 19.4 - - + +
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Residues in contact with VAL 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ARG 3.5 2.4 - - - +
84A VAL* 3.2 4.5 - - - +
85A ARG* 2.8 68.7 + - + +
87A GLU* 4.1 22.4 - - - +
89A ARG* 4.1 5.4 - - - +
93A VAL* 3.7 23.1 - - + +
94A LEU* 1.3 80.7 - - - +
96A SER* 1.3 61.4 + - - +
97A ILE* 4.0 12.3 - - + -
104A THR* 5.0 3.1 - - + -
105A LEU 3.4 5.6 - - - +
106A GLU* 4.0 17.3 - - + +
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Residues in contact with SER 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A PHE* 3.5 28.8 - - - -
78A GLN* 3.5 20.8 + - - +
82A SER* 3.1 27.5 - - - -
83A ARG 3.3 3.8 - - - -
84A VAL* 3.4 8.7 - - - +
94A LEU 4.2 0.2 - - - -
95A VAL* 1.3 72.5 - - - +
97A ILE* 1.3 60.1 + - - +
104A THR* 3.6 2.1 - - - -
105A LEU* 2.8 42.3 + - - -
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Residues in contact with ILE 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A GLY 4.3 0.3 - - - +
82A SER* 3.2 4.2 - - - -
83A ARG* 2.8 39.0 + - + +
85A ARG* 3.5 39.0 - - - +
95A VAL* 4.0 9.2 - - + -
96A SER* 1.3 79.4 - - - +
98A ARG* 1.3 72.3 + - - +
99A ARG* 4.8 8.5 - - - +
102A ARG* 3.7 35.4 - - - +
103A GLU 3.4 9.6 - - - +
104A THR* 4.2 10.5 - - + +
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Residues in contact with ARG 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ARG* 4.4 12.5 - - - +
78A GLN* 3.7 19.5 - - - +
79A PRO* 3.5 29.8 - - - +
80A PRO 4.2 10.1 + - - -
81A GLY 4.4 10.3 + - - +
82A SER* 3.6 14.6 - - - +
97A ILE* 1.3 82.9 - - - +
99A ARG* 1.3 67.1 + - - +
100A LYS 4.1 7.0 + - - -
101A PRO* 3.6 30.2 - - - +
102A ARG* 3.5 2.8 - - - -
103A GLU* 2.8 54.2 + - + +
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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