Contacts of the strand formed by residues 7 - 12 (chain B) in PDB entry 1CI1
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 PRO 7 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B PRO 3.2 8.5 - - - +
6B GLN* 1.3 89.8 - - - +
8B ILE* 1.3 63.3 + - - +
36B HIS* 4.8 0.7 - - + -
37B ASP 3.3 24.5 - - - +
38B VAL* 4.4 4.9 - - + -
39B GLN 3.1 24.0 + - - -
224B TYR* 3.4 30.7 - - + +
230B ASN* 3.2 14.4 - - + +
250B THR* 4.0 28.0 - - + +
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Residues in contact with ILE 8 (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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6B GLN 4.3 0.4 - - - +
7B PRO* 1.3 80.5 - - - +
9B ALA* 1.3 69.9 + - - +
10B ALA* 4.1 6.5 - - + +
38B VAL* 5.0 0.7 - - - -
39B GLN* 3.3 19.3 - - + +
41B VAL* 4.4 10.5 - - + -
91B TRP* 4.2 11.9 - - + -
125B ILE* 5.2 2.2 - - + -
164B VAL* 3.5 37.7 - - + -
208B ARG* 3.6 30.1 - - + +
210B LEU* 3.5 25.4 - - + +
230B ASN 3.0 6.7 + - - -
231B GLY* 3.1 6.1 - - - -
232B PHE* 2.9 24.4 + - - +
250B THR* 5.4 1.1 - - - -
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Residues in contact with ALA 9 (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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8B ILE* 1.3 73.0 - - - +
10B ALA* 1.3 59.8 + - - +
38B VAL* 4.6 6.8 - - + +
39B GLN 3.1 6.5 + - - -
40B CYS* 3.4 10.7 - - - +
41B VAL 3.1 22.5 + - - +
232B PHE* 3.8 15.0 - - + +
234B VAL* 5.7 0.2 - - - -
243B PHE* 4.1 10.4 - - + -
246B ILE* 5.4 1.1 - - + -
247B ILE* 3.7 37.0 - - + -
250B THR* 5.1 3.4 - - + -
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Residues in contact with ALA 10 (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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8B ILE* 4.3 9.9 - - + -
9B ALA* 1.3 74.5 - - - +
11B ALA* 1.3 57.8 + - - +
41B VAL* 3.5 19.5 - - + -
93B VAL* 6.4 0.2 - - + -
125B ILE* 4.4 11.2 - - + -
210B LEU* 4.5 1.3 - - + -
232B PHE 2.8 18.0 + - - +
233B LEU* 3.8 20.2 - - + -
234B VAL* 2.7 37.1 + - - +
243B PHE* 4.2 2.4 - - - -
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Residues in contact with ALA 11 (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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10B ALA* 1.3 75.2 - - - +
12B ASN* 1.3 58.4 + - - +
13B TRP* 3.5 15.0 + - - +
41B VAL 2.7 16.2 + - - +
42B VAL* 4.2 7.2 - - + -
43B ALA* 2.8 34.1 + - - +
233B LEU* 5.3 0.4 - - - -
238B SER* 3.4 26.9 - - - +
243B PHE* 3.6 17.9 - - + -
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Residues in contact with ASN 12 (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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76A THR* 3.1 26.3 + - - +
10B ALA 3.9 1.2 + - - -
11B ALA* 1.3 70.0 - - - +
13B TRP* 1.3 62.8 + - - +
14B LYS* 3.1 28.5 + - - +
43B ALA* 4.2 7.0 - - + -
66B GLN* 3.5 21.5 - - - +
93B VAL* 5.3 5.7 - - + +
96B HIS* 3.4 24.7 + - - -
233B LEU* 4.2 18.4 - - + +
234B VAL 2.9 22.4 + - - +
235B GLY* 4.0 7.8 - - - +
238B SER* 3.9 4.0 + - - -
239B LEU* 5.9 0.2 - - - +
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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