Contacts of the strand formed by residues 87 - 93 (chain A) in PDB entry 1S9D
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 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A ARG 3.2 5.9 + - - -
20A ILE* 3.2 21.2 - - - +
21A LEU 2.9 24.6 + - - -
85A THR* 3.6 9.0 - - - +
86A GLN* 1.3 81.7 - - - +
88A LEU* 1.3 61.0 + - - -
89A ILE 4.2 0.2 - - - -
119A ALA* 4.4 1.3 - - - -
120A VAL 3.4 10.5 - - - -
173A LEU* 4.6 6.5 - - - -
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Residues in contact with LEU 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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21A LEU* 3.4 22.4 - - + +
23A VAL* 3.7 34.8 - - + -
85A THR* 5.8 1.3 - - + -
87A GLY* 1.3 73.4 - - - +
89A ILE* 1.3 63.5 + - - +
107A LEU* 4.5 5.6 - - + -
110A MET* 3.9 27.1 - - + -
111A LEU* 3.8 28.7 - - + -
116A LEU* 5.0 9.2 - - + -
119A ALA* 4.7 9.6 - - + -
120A VAL 2.8 13.4 + - - +
121A LEU* 3.4 16.3 - - + +
122A LEU* 2.9 26.5 + - - +
173A LEU* 5.2 1.4 - - - +
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Residues in contact with ILE 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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20A ILE* 3.7 25.6 - - + -
21A LEU 2.7 12.1 + - - +
22A MET* 3.2 25.1 - - + -
23A VAL* 2.8 35.0 + - - +
37A LEU* 6.2 0.4 - - + -
63A PHE* 3.7 20.0 - - + -
88A LEU* 1.3 74.9 - - - +
90A PHE* 1.3 57.7 + - - +
91A VAL* 4.1 4.7 - - + -
122A LEU* 3.2 15.9 - - + +
124A PHE* 3.5 31.4 - - + -
170A LEU* 3.8 17.9 - - + -
173A LEU* 3.8 13.2 - - + -
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Residues in contact with PHE 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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23A VAL* 3.3 30.1 - - + -
24A GLY* 4.2 11.9 - - - -
25A LEU 4.9 2.0 - - - -
88A LEU* 4.0 2.0 + - + -
89A ILE* 1.3 72.1 - - - +
91A VAL* 1.3 76.6 + - - +
92A VAL* 4.1 13.0 - - + -
103A ALA* 3.4 34.3 - - + -
106A GLU* 4.2 9.2 - - + -
107A LEU* 3.5 49.6 - - + -
121A LEU* 4.1 8.5 - - + -
122A LEU 2.8 9.2 + - - +
123A VAL* 3.3 11.7 - - + +
124A PHE 2.9 25.5 + - - -
143A LEU* 4.5 17.3 - - + -
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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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22A MET* 3.6 34.1 - - + -
23A VAL 2.8 10.7 + - - +
24A GLY* 3.4 13.3 - - - -
25A LEU 4.3 0.9 + - - -
28A ALA* 3.3 42.7 - - + +
29A GLY 4.2 2.2 - - - +
30A LYS* 4.1 6.1 - - + -
33A ILE* 3.8 31.6 - - + -
89A ILE* 4.1 5.6 - - + -
90A PHE* 1.3 80.4 - - - +
92A VAL* 1.3 61.7 + - - +
103A ALA* 5.8 0.2 - - - +
124A PHE* 3.7 7.0 - - + +
126A ASN* 4.1 10.3 - - + -
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Residues in contact with VAL 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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28A ALA* 4.1 4.3 - - - -
90A PHE* 4.1 9.6 - - + -
91A VAL* 1.3 76.3 - - - +
93A ASP* 1.3 71.3 + - - +
94A SER* 3.1 4.4 + - - +
100A VAL* 4.8 11.9 - - + -
103A ALA* 4.0 23.1 - - + -
123A VAL* 4.4 2.5 - - + -
124A PHE 3.1 13.9 + - - +
125A ALA* 4.0 6.1 - - - -
126A ASN* 2.9 31.7 + - - +
139A ILE* 3.9 28.3 - - + -
143A LEU* 4.3 13.7 - - + -
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Residues in contact with ASP 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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27A ALA* 4.1 4.3 - - - +
28A ALA* 4.0 24.0 - - - +
92A VAL* 1.3 79.7 - - - +
94A SER* 1.3 56.7 + - - +
95A ASN* 2.9 25.9 + - - +
96A ASP* 3.0 44.6 + - + +
126A ASN 4.2 2.0 - - - -
127A LYS* 3.0 35.1 + - - +
130A LEU* 5.8 0.2 - - - +
134A MET* 4.6 1.7 - - - +
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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