Contacts of the strand formed by residues 73 - 78 (chain B) in PDB entry 1IVV
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 73 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32B LEU* 3.4 27.9 - - + +
37B LYS* 5.3 7.4 - - - +
62B VAL 3.8 0.3 - - - +
63B PHE* 3.6 2.6 - - - -
64B ILE* 2.8 39.7 + - + +
71B ARG 4.4 4.7 - - - +
72B PRO* 1.3 80.3 - - - +
74B GLU* 1.3 61.1 + - - +
75B VAL* 4.1 10.0 + - + +
87B ALA* 3.9 15.4 + - - +
88B VAL* 3.0 12.3 - - - +
89B GLU* 2.9 36.0 + - + +
90B LEU* 3.9 7.4 - - - +
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Residues in contact with GLU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ARG* 2.9 41.0 + - + +
62B VAL 3.4 3.1 - - - +
63B PHE* 3.5 22.9 - - + -
73B GLN* 1.3 72.8 - - - +
75B VAL* 1.3 63.3 + - - +
76B THR* 5.0 2.3 + - - +
86B SER* 4.5 0.5 + - - -
87B ALA* 3.2 2.3 + - - -
88B VAL* 2.9 41.2 + - + +
90B LEU* 3.9 21.2 - - + +
556B ASP* 4.3 3.2 - - - +
557B PHE* 3.5 17.9 - - + -
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Residues in contact with VAL 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LEU* 3.8 11.4 - - + -
32B LEU* 4.2 7.4 - - + -
60B PHE 3.8 0.5 - - - +
61B ARG* 3.3 4.3 - - - +
62B VAL* 2.7 44.0 + - + +
64B ILE* 3.8 26.2 - - + -
73B GLN* 4.2 11.2 - - + +
74B GLU* 1.3 81.3 - - - +
76B THR* 1.3 65.6 + - - +
77B VAL* 3.6 24.2 - - + -
84B VAL* 4.0 10.1 - - + -
86B SER 3.3 12.1 - - - +
87B ALA* 3.5 16.8 - - + -
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Residues in contact with THR 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B LEU* 3.7 22.4 - - + +
59B ARG* 4.2 14.1 - - + +
60B PHE 3.3 10.8 - - - +
61B ARG* 3.8 17.2 - - - +
74B GLU* 5.0 2.1 + - - -
75B VAL* 1.3 74.3 - - - +
77B VAL* 1.3 59.9 + - - +
84B VAL 3.6 0.9 - - - -
85B ILE* 2.7 48.2 + - + -
86B SER* 3.0 26.4 + - - +
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Residues in contact with VAL 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B VAL* 3.9 34.8 - - + -
26B ILE* 4.2 13.9 - - + -
27B LEU* 3.7 19.1 - - + -
59B ARG* 3.1 5.0 - - - +
60B PHE* 2.9 39.1 + - + +
62B VAL* 5.4 1.8 - - + -
75B VAL* 3.6 20.9 - - + +
76B THR* 1.3 79.5 - - - +
78B SER* 1.3 59.8 + - - +
79B VAL 3.5 6.7 + - - +
83B THR 3.3 13.5 - - - +
84B VAL* 4.2 9.4 - - + -
85B ILE* 4.1 4.9 - - - +
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Residues in contact with SER 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ILE* 4.0 0.3 - - - +
57B ASP* 2.7 25.5 + - - -
58B ARG 3.7 5.2 - - - -
59B ARG* 4.1 4.3 - - - -
77B VAL* 1.3 72.8 - - - +
79B VAL* 1.3 51.6 + - - +
80B THR 3.0 1.3 - - - -
81B ASN* 2.9 26.4 + - - -
82B GLY* 2.7 32.7 + - - -
83B THR* 2.9 28.0 + - - +
85B ILE* 3.8 17.5 - - - +
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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