Contacts of the strand formed by residues 87 - 92 (chain A) in PDB entry 4GK6
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 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A LEU* 3.9 34.3 - - + +
41A VAL 3.4 7.9 - - - +
42A GLY* 4.1 12.6 - - - +
82A TYR* 5.4 3.2 + - - +
85A GLU* 3.4 36.6 + - - +
86A VAL* 1.3 82.7 - - - +
88A VAL* 1.3 64.6 + - - +
89A ASN* 4.2 2.9 + - - -
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Residues in contact with VAL 88 (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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25A LEU* 5.3 0.2 - - + -
39A THR 3.4 0.3 - - - +
40A LEU* 3.8 2.5 - - - -
41A VAL* 2.8 35.1 + - - +
43A THR* 3.8 24.9 - - + -
57A VAL* 4.3 13.0 - - + -
71A ILE* 3.7 27.8 - - + -
86A VAL* 4.8 2.9 - - + -
87A LYS* 1.3 78.5 - - - +
89A ASN* 1.3 61.3 + - - +
90A LEU* 3.2 36.4 + - + +
107A ILE* 4.4 6.3 - - + -
108A ALA* 4.2 18.4 - - + -
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Residues in contact with ASN 89 (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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38A ARG* 5.6 3.4 - - + +
39A THR 3.8 5.7 - - - -
40A LEU* 3.5 30.2 + - - +
71A ILE* 3.3 6.0 - - - +
72A VAL* 2.9 38.8 + - + +
73A ASN* 3.6 30.2 + - - +
87A LYS 4.2 2.6 + - - -
88A VAL* 1.3 70.5 - - - +
90A LEU* 1.3 61.5 + - - +
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Residues in contact with LEU 90 (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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33A ILE* 3.8 12.8 - - + +
38A ARG* 3.1 6.5 - - - +
39A THR 2.9 36.9 + - - +
41A VAL* 3.9 23.3 - - + -
69A LEU* 4.2 12.1 - - + -
70A SER 3.4 12.8 - - - +
71A ILE* 4.3 2.5 - - + -
88A VAL* 3.5 31.0 - - + +
89A ASN* 1.3 71.8 - - - +
91A ILE* 1.3 58.9 + - - +
101A ILE* 3.7 29.4 - - + -
107A ILE* 3.8 31.9 - - + +
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Residues in contact with ILE 91 (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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33A ILE* 4.6 1.3 - - - -
36A GLY* 4.7 9.4 - - - +
37A ARG 3.5 15.5 - - - +
38A ARG* 4.1 7.4 - - + +
68A GLY 3.4 3.3 - - - +
69A LEU* 3.6 8.6 - - - +
70A SER* 3.0 52.6 + - - +
71A ILE 4.1 0.9 - - - +
72A VAL* 3.8 30.5 - - + +
90A LEU* 1.3 74.3 - - - +
92A ASN* 1.3 71.8 + - - +
93A LEU* 3.8 22.2 - - + -
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Residues in contact with ASN 92 (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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33A ILE* 3.0 32.2 + - + +
34A GLU 3.5 14.1 - - - +
35A PRO* 3.5 14.5 - - - +
36A GLY* 2.9 33.6 + - - -
37A ARG 3.0 7.3 + - - -
67A VAL 4.0 0.2 - - - +
68A GLY 3.8 2.2 - - - -
91A ILE* 1.3 73.2 - - - +
93A LEU* 1.3 59.6 + - - +
94A ASP* 2.8 23.8 + - - +
97A VAL 3.0 23.2 + - - -
99A ILE* 3.4 24.5 - - + +
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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