Contacts of the strand formed by residues 32 - 38 (chain A) in PDB entry 2IAF
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 ARG 32 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A THR* 3.6 2.8 - - - +
31A GLN* 1.3 82.7 - - - +
33A VAL* 1.3 72.4 + - - +
34A LYS* 3.8 13.6 - - - +
92A ILE* 4.0 4.5 - - - -
93A PRO 4.7 5.2 - - - +
98A THR* 3.0 28.5 + - - -
99A ASP* 2.9 33.3 + - - +
119A ALA* 3.4 3.8 - - - -
120A PHE* 2.8 74.9 + - + +
121A ASP 4.9 2.7 - - - +
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Residues in contact with VAL 33 (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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17A PHE* 4.6 13.7 - - + -
21A LEU* 5.2 0.9 - - + -
30A THR* 3.9 16.8 - - + -
32A ARG* 1.3 81.7 - - - +
34A LYS* 1.3 63.2 + - - +
35A VAL* 5.2 1.1 - - + -
58A LEU* 4.2 17.5 - - + -
84A LEU* 3.7 28.7 - - + -
86A LEU* 4.0 14.1 - - + -
92A ILE* 3.9 11.2 - - + +
93A PRO 5.2 0.8 + - - -
94A PHE* 4.7 8.2 - - + -
99A ASP* 3.3 26.6 + - - +
117A PHE* 6.4 0.7 - - + -
118A SER 3.1 12.1 - - - +
119A ALA* 4.6 2.5 - - + -
120A PHE* 4.8 0.7 - - - -
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Residues in contact with LYS 34 (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 ARG* 3.8 13.7 - - - +
33A VAL* 1.3 75.9 - - - +
35A VAL* 1.3 74.7 + - - +
36A GLU* 4.0 30.9 + - + -
98A THR 3.6 22.9 - - - +
99A ASP 3.3 7.6 - - - +
101A LEU* 4.6 9.7 - - + +
116A ARG 3.7 0.9 - - - +
117A PHE* 3.5 4.0 - - - +
118A SER* 2.9 38.3 + - - +
120A PHE* 3.9 31.4 - - + -
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Residues in contact with VAL 35 (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* 5.2 2.2 - - + -
34A LYS* 1.3 82.0 - - - +
36A GLU* 1.3 63.2 + - - +
37A LEU* 4.1 22.4 - - + -
54A ILE* 4.0 21.8 - - + -
58A LEU* 3.9 18.8 - - + -
94A PHE* 6.0 1.1 - - + -
99A ASP 2.8 10.6 + - - +
100A PHE* 3.4 19.4 + - + -
101A LEU* 2.8 31.8 + - - +
115A MSE 5.0 0.2 - - + -
116A ARG 3.3 7.4 - - - +
117A PHE* 3.8 31.4 - - + -
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Residues in contact with GLU 36 (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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34A LYS* 4.0 34.8 + - + +
35A VAL* 1.3 79.1 - - - +
37A LEU* 1.3 63.0 + - - +
38A TYR* 3.7 23.6 + - + +
101A LEU* 3.5 17.3 - - + +
103A LEU* 4.0 16.6 - - + +
115A MSE 3.3 6.4 - - - +
116A ARG* 2.8 70.7 + - + +
118A SER* 4.4 1.7 + - - -
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Residues in contact with LEU 37 (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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35A VAL* 4.1 3.8 - - + -
36A GLU* 1.3 75.4 - - - +
38A TYR* 1.3 60.1 + - - +
41A LEU* 3.8 18.8 - - + +
42A ALA* 3.6 14.6 - - - +
50A THR* 3.9 17.7 - - + -
54A ILE* 3.7 25.8 - - + -
100A PHE* 3.6 22.4 - - + -
101A LEU 2.8 14.5 + - - +
102A PHE* 3.5 31.2 - - + -
103A LEU* 2.8 35.5 + - - +
114A GLY 3.8 0.9 - - - -
115A MSE 3.8 18.8 - - + -
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Residues in contact with TYR 38 (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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36A GLU* 3.7 29.3 + - + -
37A LEU* 1.3 78.3 - - - +
39A GLY* 1.3 70.7 + - - +
40A SER 3.2 0.3 + - - -
41A LEU* 3.0 18.4 + - - +
42A ALA* 3.0 4.0 + - - -
103A LEU* 3.6 21.5 - - + +
106A GLU* 3.5 47.0 + - + +
107A LEU 4.1 2.7 - - - -
108A LEU* 3.5 51.1 - - + +
112A SER 3.3 7.1 - - - +
114A GLY* 3.0 20.4 + - - +
116A ARG* 2.6 32.7 + - + -
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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