Contacts of the strand formed by residues 86 - 92 (chain A) in PDB entry 1KSG
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 GLY 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A ARG 3.3 3.6 + - - -
19A LEU* 3.3 19.9 - - - +
20A LEU 2.9 26.9 + - - +
84A THR* 3.3 6.6 - - - +
85A ASP* 1.3 83.2 - - - +
87A LEU* 1.3 62.5 + - - -
88A ILE* 4.9 0.7 - - - -
118A ALA* 4.6 0.2 - - - -
119A THR 3.5 9.2 - - - -
172A LEU* 4.4 4.3 - - - -
176A ILE* 4.0 5.8 - - - -
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Residues in contact with LEU 87 (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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20A LEU* 3.5 26.2 - - + +
22A LEU* 4.0 26.5 - - + -
84A THR* 4.7 1.1 - - + -
86A GLY* 1.3 73.6 - - - -
88A ILE* 1.3 64.5 + - - +
89A TRP* 4.1 2.0 - - + +
106A LEU* 5.2 1.8 - - + -
109A LEU* 4.4 12.3 - - + -
110A LEU* 4.1 21.3 - - + -
115A LEU* 4.1 24.0 - - + -
118A ALA* 4.2 14.4 - - + +
119A THR 2.8 11.5 + - - +
120A LEU* 3.4 24.0 - - + +
121A LEU* 3.0 24.8 + - - +
172A LEU* 4.8 0.7 - - - +
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Residues in contact with ILE 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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19A LEU* 4.4 16.4 - - + -
20A LEU 2.8 15.7 + - - +
21A MET* 3.3 28.0 - - + +
22A LEU* 2.9 30.5 + - - +
36A PHE* 5.5 3.1 - - + -
64A ILE* 5.2 5.2 - - + -
86A GLY 4.8 3.4 - - - +
87A LEU* 1.3 77.4 - - - +
89A TRP* 1.3 61.7 + - - +
90A VAL* 3.8 3.1 + - + -
121A LEU* 3.4 10.5 - - + +
123A PHE* 3.7 30.3 - - + -
169A ILE* 4.0 17.7 - - + -
172A LEU* 3.8 29.8 - - + -
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Residues in contact with TRP 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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22A LEU* 3.5 5.6 - - + -
23A GLY* 3.5 37.0 - - - -
24A LEU 4.5 2.9 - - - -
77A TRP* 3.8 10.1 - + - -
87A LEU* 4.1 3.7 - - + -
88A ILE* 1.3 71.4 - - - +
90A VAL* 1.3 61.1 + - - +
91A VAL* 3.5 21.5 - - + +
102A CYS* 3.1 50.9 + - - -
105A GLU* 3.4 25.4 - - + -
106A LEU* 3.6 33.4 - - + +
109A LEU* 3.5 30.7 - - + -
120A LEU* 4.2 8.1 - - + -
121A LEU 2.9 13.4 + - - +
122A ILE* 3.4 11.9 - - + +
123A PHE 2.9 24.6 + - - -
142A LEU* 4.3 9.5 - - + +
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Residues in contact with VAL 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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21A MET* 3.7 27.8 - - + -
22A LEU 3.0 5.5 + - - -
23A GLY* 3.7 12.0 - - - -
24A LEU 4.4 1.0 + - - -
27A ALA* 3.4 41.4 - - + +
28A GLY 3.9 3.1 - - - -
29A LYS* 3.5 34.3 - - + +
32A ILE* 4.0 18.8 - - + -
88A ILE* 4.4 6.3 - - + -
89A TRP* 1.3 75.8 + - - +
91A VAL* 1.3 66.2 + - - +
102A CYS* 5.2 0.7 - - - -
123A PHE* 3.8 5.4 - - + +
125A ASN* 4.1 7.2 - - + -
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Residues in contact with VAL 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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27A ALA* 4.3 5.2 - - - -
89A TRP* 3.5 17.5 - - + +
90A VAL* 1.3 77.2 - - - +
92A ASP* 1.3 73.2 - - - +
93A SER 3.2 3.0 + - - +
99A MET* 4.3 19.3 - - - -
102A CYS* 3.4 31.2 - - + -
122A ILE* 4.5 2.7 - - + -
123A PHE 2.9 14.3 + - - +
124A ALA* 4.6 4.0 - - - -
125A ASN* 2.9 30.0 + - - +
138A ILE* 4.3 15.9 - - + -
142A LEU* 4.1 11.0 - - + -
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Residues in contact with ASP 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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26A ASN* 3.8 7.6 + - - +
27A ALA* 4.2 21.4 - - - +
91A VAL* 1.3 78.1 - - - +
93A SER* 1.3 62.7 + - - +
94A ALA* 2.7 37.1 + - - +
95A ASP* 2.9 41.1 + - + +
99A MET* 4.6 3.3 - - - +
125A ASN 4.2 2.2 - - - -
126A LYS* 2.6 39.6 + - + +
129A LEU* 5.6 0.2 - - - +
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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