Contacts of the strand formed by residues 11 - 14 (chain B) in PDB entry 5ICN
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 VAL 11 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ARG 4.0 4.4 + - - +
10B LYS* 1.3 79.5 - - - +
12B CYS* 1.3 65.7 + - - +
50B LYS 5.8 0.4 + - - -
51B MET* 3.4 25.9 - - + +
52B GLU* 3.0 28.8 + - - +
131B ILE* 3.4 13.9 - - + +
133B VAL* 4.0 25.1 - - + -
316B THR* 5.4 1.1 - - + -
319B ALA* 3.4 36.3 - - + +
320B LEU* 3.8 22.8 - - + +
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Residues in contact with CYS 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LYS* 4.8 2.5 - - - -
11B VAL* 1.3 79.4 - - - +
13B TYR* 1.3 57.3 + - - +
14B TYR* 4.0 19.3 - - + -
52B GLU* 3.3 24.0 - - - +
54B TYR* 4.2 6.5 - - + -
123B LYS* 4.0 15.9 - - + -
128B GLN 4.6 2.9 - - - -
129B THR* 3.2 27.4 - - - +
131B ILE 3.0 11.6 + - - +
132B ALA* 3.3 4.9 - - + -
133B VAL* 2.7 33.8 + - - +
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Residues in contact with TYR 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B VAL 4.2 0.4 + - - -
12B CYS* 1.3 74.1 - - - +
14B TYR* 1.3 62.8 + - - +
15B TYR* 3.7 17.4 - - + -
35B ILE* 4.6 3.5 + - - +
39B HIS* 3.3 46.5 + + - +
42B LEU* 3.4 32.4 - - + +
48B TYR* 5.5 1.3 - + - -
51B MET* 3.7 28.9 - - + -
52B GLU 2.8 9.7 + - - +
53B ILE* 3.4 27.3 - - + +
54B TYR* 2.8 31.2 + - - +
133B VAL* 3.6 19.3 - - + -
135B TRP* 3.6 25.3 - + - -
316B THR* 5.0 0.7 - - + -
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Residues in contact with TYR 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A GLU* 2.8 29.9 + - + -
12B CYS* 4.0 22.4 - - + -
13B TYR* 1.3 82.0 - - - +
15B TYR* 1.3 64.5 + - - +
54B TYR* 3.3 33.9 - + + -
56B PRO* 4.3 14.6 - - + -
116B GLY* 4.0 19.3 - - - -
119B ALA* 3.7 17.7 + - + -
120B SER* 3.6 30.5 - - - -
123B LYS* 3.1 25.5 - - + +
132B ALA* 4.7 0.2 - - + -
133B VAL 2.9 22.9 + - - +
134B ASN* 3.8 18.3 - - + +
135B TRP 4.7 1.7 + - - -
136B ALA* 5.6 0.9 + - - +
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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
------------------------------------------------------------
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