Contacts of the strand formed by residues 97 - 104 (chain A) in PDB entry 1I3V
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 ALA 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A ARG* 3.9 15.5 - - + -
39A GLN 3.5 26.0 - - - +
40A ALA* 3.8 4.3 - - + +
41A PRO* 4.9 3.1 - - - -
95A ASP 3.3 3.6 + - - +
96A THR* 1.3 80.3 - - - +
98A VAL* 1.3 63.1 + - - +
99A TYR* 3.6 17.7 - - + -
124A GLN* 3.3 9.6 - - - +
125A VAL 2.9 30.4 + - - +
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Residues in contact with VAL 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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38A ARG* 3.2 2.6 - - - -
39A GLN 2.9 33.6 + - - +
97A ALA* 1.3 73.6 - - - +
99A TYR* 1.3 62.5 + - - +
100A TYR* 3.5 37.8 - - + +
121A GLN 4.9 0.7 - - - +
122A GLY* 3.7 4.5 - - - -
123A THR 3.4 21.8 - - - +
124A GLN* 3.2 30.5 - - + +
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Residues in contact with TYR 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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6A GLU* 4.0 2.3 - - - +
20A LEU* 3.5 29.8 - - + -
36A TRP* 4.6 4.9 - + + -
37A PHE 3.4 4.3 - - - +
38A ARG* 2.8 32.5 + - + -
48A LEU* 3.6 27.4 - - + -
73A PHE* 4.4 1.9 - + - -
86A LEU* 4.3 3.8 - - + -
88A MET* 3.7 22.6 - - + -
95A ASP* 2.6 35.1 + - - +
97A ALA* 3.6 19.3 - - + -
98A VAL* 1.3 74.0 - - - +
100A TYR* 1.3 59.9 + - - +
122A GLY* 3.2 3.1 - - - -
123A THR* 2.8 38.8 + - + +
125A VAL* 3.7 26.7 - - + -
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Residues in contact with TYR 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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6A GLU* 3.4 5.6 - - - +
36A TRP* 3.4 9.3 - - - -
37A PHE* 2.7 38.8 + - + +
38A ARG* 4.7 2.9 - - - -
39A GLN* 4.4 15.6 + - + -
45A ARG* 3.1 39.7 + - - -
98A VAL* 3.5 38.1 - - + +
99A TYR* 1.3 76.3 - - - +
101A CYS* 1.3 60.5 + - - +
119A TRP* 4.2 21.3 - + + -
120A GLY 3.9 13.2 - - - -
121A GLN 3.5 20.7 + - - -
122A GLY* 3.5 13.0 - - - -
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Residues in contact with CYS 101 (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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4A LEU* 4.0 11.3 - - - +
6A GLU* 3.0 26.3 + - - +
22A CYS* 2.2 53.6 - - + -
34A ILE* 4.3 3.4 - - + -
35A GLY 3.1 11.2 - - - +
36A TRP* 4.1 12.1 - - + -
100A TYR* 1.3 75.0 - - - +
102A ALA* 1.3 61.1 + - - +
119A TRP* 3.9 3.2 - - - -
120A GLY 3.0 25.3 + - - -
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Residues in contact with ALA 102 (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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4A LEU* 3.9 5.2 - - - -
34A ILE* 3.4 7.3 - - - +
35A GLY 2.9 30.0 + - - -
37A PHE* 4.3 5.2 - - + -
101A CYS* 1.3 76.1 - - - +
103A ALA* 1.3 62.6 + - - +
116A TRP* 3.8 19.5 - - + -
118A TYR 3.1 13.5 - - - +
119A TRP* 3.7 33.9 - - + -
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Residues in contact with ALA 103 (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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2A VAL* 4.5 4.3 - - + -
4A LEU* 3.8 13.7 - - + +
32A TYR* 4.0 19.5 - - + -
33A VAL 3.3 5.4 - - - +
34A ILE* 3.8 18.8 - - + -
102A ALA* 1.3 74.9 - - - +
104A LYS* 1.3 61.0 + - - +
116A TRP* 3.7 2.6 - - - -
117A ASN* 3.0 24.0 + - - +
118A TYR* 2.8 26.6 + - + +
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Residues in contact with LYS 104 (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 TYR* 3.6 5.9 - - - -
33A VAL* 2.8 41.7 + - + +
50A THR* 6.0 0.9 - - - -
64A ARG* 5.7 2.2 - - - +
103A ALA* 1.3 74.4 - - - +
105A THR* 1.3 64.8 + - - +
106A THR* 3.3 23.7 + - - +
107A THR 3.7 7.2 + - - -
108A TRP 2.6 31.6 + - - +
109A GLY* 4.6 0.4 - - - -
110A GLY* 3.9 11.5 - - - +
115A ASN 4.2 14.6 - - - +
116A TRP* 3.3 50.3 - - + +
117A ASN* 3.3 16.2 - - - +
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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