Contacts of the strand formed by residues 93 - 100 (chain A) in PDB entry 1RS2
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 GLU 93 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A THR 4.0 0.7 - - - +
35A LEU* 3.5 0.3 - - - -
36A LYS* 2.7 53.6 + - + +
85A ASN* 4.6 0.2 - - - -
91A VAL* 3.3 6.7 - - - +
92A MET* 1.3 83.4 - - - +
94A THR* 1.3 68.1 + - - +
95A LYS* 5.5 6.2 - - + +
117A VAL* 3.3 34.7 - - + +
118A ARG 3.6 9.6 - - - +
119A GLU* 3.9 16.5 - - + +
120A ASN 4.0 1.1 - - - +
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Residues in contact with THR 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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33A VAL* 4.7 1.6 - - + -
34A THR 3.7 2.0 - - - -
35A LEU* 3.0 30.3 - - + +
81A ALA* 4.1 13.0 - - - +
84A ILE* 3.4 13.0 - - + +
85A ASN* 2.9 29.5 + - - -
91A VAL* 3.1 6.1 - - - +
93A GLU* 1.3 75.3 - - - +
95A LYS* 1.3 60.8 + - - +
96A VAL* 4.0 20.5 + - + -
116A ILE 3.9 0.9 - - - +
117A VAL* 3.5 0.5 - - - -
118A ARG* 2.7 44.1 + - - +
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Residues in contact with LYS 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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32A ASP 3.7 1.2 - - - +
33A VAL* 3.5 7.4 - - - +
34A THR* 2.9 57.0 + - - +
93A GLU* 5.0 4.7 - - + +
94A THR* 1.3 73.2 - - - +
96A VAL* 1.3 64.6 + - - +
97A ARG* 5.8 0.2 - - + -
115A GLU* 3.6 31.3 + - + +
116A ILE 3.2 11.0 - - - +
117A VAL* 3.8 25.4 - - + +
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Residues in contact with VAL 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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31A VAL* 4.3 9.0 - - + -
32A ASP 3.7 1.3 - - - -
33A VAL* 4.3 5.6 - - + -
77A ALA* 3.6 45.7 - - + +
80A ILE* 4.1 23.6 - - + -
81A ALA* 3.9 22.9 - - + +
94A THR* 4.0 9.6 - - + -
95A LYS* 1.3 77.3 - - - +
97A ARG* 1.3 62.7 + - - +
98A ILE* 4.1 9.2 - - + -
114A ILE 4.1 0.3 - - - +
115A GLU* 3.2 4.6 - - - -
116A ILE* 2.8 41.5 + - + +
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Residues in contact with ARG 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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30A LYS 3.7 0.7 - - - +
31A VAL* 3.3 6.9 - - - +
32A ASP* 2.9 62.4 + - + +
95A LYS* 5.3 0.9 - - + +
96A VAL* 1.3 74.9 - - - +
98A ILE* 1.3 67.8 + - - +
99A THR* 4.1 17.4 + - - +
114A ILE 3.5 11.4 - - - +
115A GLU* 3.6 37.1 + - + +
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Residues in contact with ILE 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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29A PHE* 4.3 8.3 - - + -
30A LYS 3.3 7.4 - - - +
31A VAL* 3.9 13.9 - - + -
65A MET* 4.1 21.5 - - + -
73A LEU* 3.6 33.7 - - + +
76A LEU* 3.8 16.8 - - + -
77A ALA* 3.7 34.5 - - + +
80A ILE* 4.4 4.0 - - + -
96A VAL* 4.1 8.0 - - + -
97A ARG* 1.3 79.9 - - - +
99A THR* 1.3 64.2 + - - +
113A GLY* 3.4 4.5 - - - -
114A ILE* 3.1 32.9 + - + +
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Residues in contact with THR 99 (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 ILE 4.3 0.3 - - - +
29A PHE* 3.7 6.6 - - - +
30A LYS* 2.8 53.5 + - + +
32A ASP* 5.4 0.2 + - - -
73A LEU* 5.0 0.2 - - - -
97A ARG* 4.1 19.2 + - - +
98A ILE* 1.3 77.1 + - - +
100A LYS* 1.3 63.0 + - - +
101A GLU* 3.7 29.7 + - + +
111A GLY* 4.1 13.0 - - - -
112A VAL 3.4 11.7 - - - +
113A GLY* 5.4 0.5 - - - -
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Residues in contact with LYS 100 (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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16A HIS 4.2 2.9 + - - -
22A GLU* 2.6 30.9 + - - -
27A GLN* 3.0 28.7 - - + +
28A ILE 4.7 3.8 - - - +
29A PHE* 3.6 32.8 - - + -
73A LEU* 4.1 21.7 - - + +
98A ILE 4.3 0.4 + - - -
99A THR* 1.3 72.3 - - - +
101A GLU* 1.3 60.7 + - - +
102A ASN 3.1 4.7 - - - -
103A PRO* 3.2 19.3 - - + +
104A PRO* 4.9 1.4 - - - +
112A VAL* 2.7 40.9 + - + +
1001A 209 3.0 32.8 + - + +
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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