Contacts of the strand formed by residues 27 - 32 (chain C) in PDB entry 4BEJ
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 27 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C ILE* 6.2 0.2 - - + -
12C GLN* 2.7 38.9 + - - +
21C ASP* 3.8 21.0 + - - -
25C LEU* 3.5 16.8 + - - +
26C PRO* 1.3 76.0 - - - +
28C ILE* 1.3 67.2 + - - +
29C VAL* 4.2 3.5 + - + +
64C ILE* 5.1 2.4 - - - +
143C THR* 5.7 3.6 - - + +
145C VAL* 3.7 23.4 - - + +
173C PHE* 4.5 18.8 + - - -
176C ASN* 5.6 0.8 - - - +
178C ASN 3.8 3.1 + - - +
179C SER* 3.5 20.1 + - - +
180C ILE* 3.0 25.9 + - - +
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Residues in contact with ILE 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C GLN* 1.3 82.2 - - - +
29C VAL* 1.3 63.6 + - - +
30C VAL 4.1 0.2 + - - -
142C LEU* 4.4 12.3 - - + -
143C THR 4.3 7.3 + - - +
144C LEU* 3.7 28.9 - - + +
145C VAL* 2.9 27.9 + - - +
180C ILE* 3.4 36.6 - - + +
182C LEU* 3.7 31.2 - - + +
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Residues in contact with VAL 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C GLN* 4.2 7.8 - - + +
28C ILE* 1.3 76.2 - - - +
30C VAL* 1.3 62.5 + - - +
31C VAL* 3.8 5.6 + - + +
145C VAL* 3.5 23.8 - - + +
147C LEU* 4.1 11.0 - - + -
173C PHE* 4.0 29.4 - - + -
174C ILE* 4.6 20.9 - - + -
179C SER* 4.4 17.7 - - - +
180C ILE 3.1 13.6 + - - +
181C ILE* 3.8 6.2 - - + -
182C LEU 2.9 24.5 + - - +
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Residues in contact with VAL 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C VAL* 1.3 74.7 - - - +
31C VAL* 1.3 64.0 + - - +
32C GLY 4.2 0.7 + - - -
38C LYS* 4.5 13.5 - - + +
41C VAL* 5.9 0.9 - - + -
42C LEU* 4.2 17.5 - - + -
144C LEU* 4.0 26.7 - - + -
145C VAL 3.0 13.6 + - - +
146C ASP* 4.1 12.4 - - - +
147C LEU* 3.6 24.4 + - - +
182C LEU* 3.4 28.3 - - + +
184C VAL* 3.7 27.4 - - + -
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Residues in contact with VAL 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C VAL* 4.5 9.9 - - + +
30C VAL* 1.3 79.3 - - - +
32C GLY* 1.3 61.1 + - - +
38C LYS* 4.5 1.3 - - - -
147C LEU* 4.1 13.2 - - + -
150C MET* 4.1 14.4 - - + -
170C ILE* 3.9 24.5 - - + -
174C ILE* 4.5 15.0 - - + -
181C ILE* 4.7 9.2 - - + -
182C LEU 2.9 9.2 + - - +
183C ALA* 3.5 3.3 - - - -
184C VAL* 2.9 25.2 + - - -
196C ALA* 3.7 12.8 - - + +
199C ILE* 3.8 28.3 - - + -
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Residues in contact with GLY 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C VAL* 1.3 78.0 - - - +
33C THR* 1.3 66.9 + - - -
36C SER* 3.7 5.6 - - - -
38C LYS* 3.4 14.9 - - - +
147C LEU 5.7 0.2 + - - -
148C PRO 4.7 0.7 + - - +
149C GLY* 3.2 21.8 - - - -
150C MET* 3.5 9.5 + - - +
170C ILE* 5.8 0.4 - - - +
184C VAL* 3.6 15.0 - - - -
196C ALA* 4.2 5.6 - - - -
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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