Contacts of the strand formed by residues 75 - 79 (chain A) in PDB entry 2IHU
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 GLN 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A GLY 5.5 3.2 + - - -
27A VAL* 4.5 17.8 - - - +
28A GLY 4.9 2.6 + - - -
29A LYS 4.7 4.0 + - - +
31A PHE* 5.4 1.1 - - + -
64A ALA* 3.5 24.2 - - + +
67A LEU* 3.5 28.4 - - + +
68A ALA* 3.5 21.5 - - + +
71A THR* 3.2 24.9 + - - +
73A ARG* 3.3 25.8 + - - +
74A PRO* 1.3 78.6 + - - +
76A ALA* 1.3 63.1 + - - +
101A PRO 3.2 6.6 + - - +
102A VAL* 3.6 3.2 - - + -
103A ILE* 2.8 28.9 + - - +
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Residues in contact with ALA 76 (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* 4.2 25.8 - - + -
27A VAL* 4.1 19.3 - - + +
29A LYS 3.9 7.4 + - - +
30A VAL* 3.6 9.9 - - + -
31A PHE* 3.1 31.2 + - - -
64A ALA* 4.1 4.6 - - - +
75A GLN* 1.3 79.8 - - - +
77A CYS* 1.3 60.8 + - - +
103A ILE* 3.2 10.8 - - + +
105A LEU* 4.7 2.7 - - + -
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Residues in contact with CYS 77 (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 VAL* 4.3 2.5 - - - -
31A PHE 2.9 12.1 - - - +
60A ALA 3.8 18.6 - - - +
61A GLY* 3.9 10.3 - - - -
64A ALA* 4.3 0.9 - - + -
76A ALA* 1.3 74.7 - - - +
78A TRP* 1.3 60.8 + - - +
88A LEU* 3.7 24.7 - - + -
91A GLY 6.3 0.2 - - - -
92A ILE* 5.5 1.8 - - - -
102A VAL* 3.8 24.0 - - - -
103A ILE 3.1 7.9 + - - +
104A ALA* 3.8 15.7 - - - -
105A LEU* 3.0 31.1 + - - +
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Residues in contact with TRP 78 (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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18A LEU* 3.7 16.8 - - + -
19A LEU* 5.9 1.1 - - + -
30A VAL* 3.8 15.9 - - + -
31A PHE 2.8 7.2 + - - +
32A GLY* 3.2 3.5 - - - -
33A VAL 3.2 30.7 + - - -
34A VAL* 4.3 7.8 - - + +
37A GLU* 2.9 33.2 + - + +
41A ILE* 3.7 33.9 - - + -
43A PHE* 3.5 28.3 - + - -
51A PHE* 3.9 8.3 - - + -
57A GLU* 4.6 1.0 - - - +
77A CYS* 1.3 76.5 - - - +
79A ALA* 1.3 72.1 + - - +
88A LEU* 4.4 6.4 - - - +
105A LEU* 3.3 29.2 - - + -
107A ALA 4.9 4.5 - - - -
168A LEU* 3.5 31.6 - - + -
173A LEU* 3.9 10.8 - - + -
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Residues in contact with ALA 79 (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 3.6 6.5 - - - -
57A GLU* 3.8 11.4 - - + -
78A TRP* 1.3 87.2 + - - +
80A THR* 1.3 61.4 + - - +
84A GLY 3.3 29.8 - - - +
85A MET* 3.9 2.9 - - - +
88A LEU* 3.8 17.2 - - + +
105A LEU 2.9 8.2 + - - +
106A ALA* 3.1 4.6 - - + -
107A ALA 3.0 22.0 + - - -
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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