Contacts of the strand formed by residues 27 - 32 (chain A) in PDB entry 4H1V
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A GLN* 2.9 36.5 + - - +
25A LEU* 3.3 24.1 + - + +
26A PRO* 1.3 75.2 - - - +
28A ILE* 1.3 63.2 - - - +
29A VAL* 3.9 14.2 + - + +
64A ILE* 5.1 2.8 - - - +
143A THR* 5.7 2.5 - - + -
145A VAL* 3.7 21.4 - - + +
173A PHE* 4.5 16.2 + - - -
176A ASN* 4.2 14.8 - - - +
178A ASN 3.5 3.3 + - - +
179A SER* 3.3 6.9 - - - -
180A ILE* 2.8 25.4 + - - +
293A LEU* 4.3 8.5 - - - -
296A HIS* 4.4 2.0 - - - -
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Residues in contact with ILE 28 (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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27A GLN* 1.3 75.6 - - - +
29A VAL* 1.3 63.6 + - - +
142A LEU* 4.1 7.9 - - + -
143A THR 4.1 7.0 + - - +
144A LEU* 3.7 29.0 - - + -
145A VAL* 2.8 31.0 + - - +
180A ILE* 3.3 29.6 - - + +
182A LEU* 3.8 26.0 - - + -
289A LEU* 4.0 37.5 - - + +
292A LEU* 5.1 3.6 - - + -
293A LEU* 4.1 19.5 - - + +
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Residues in contact with VAL 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLN* 4.3 14.6 - - + +
28A ILE* 1.3 76.5 - - - +
30A VAL* 1.3 63.6 + - - +
31A VAL* 3.5 3.1 + - + -
145A VAL* 3.6 14.4 - - + +
147A LEU* 3.5 35.9 - - + -
173A PHE* 4.3 12.3 - - + +
174A ILE* 3.7 21.1 - - + -
179A SER* 3.9 24.7 - - - -
180A ILE 2.7 13.0 + - - +
181A ILE* 3.6 4.0 - - - +
182A LEU* 2.8 25.8 + - - -
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Residues in contact with VAL 30 (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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29A VAL* 1.3 71.6 - - - +
31A VAL* 1.3 63.0 + - - +
32A GLY 4.0 1.4 + - - -
38A LYS* 4.0 17.9 - - + +
41A VAL* 6.0 1.8 - - + -
42A LEU* 4.5 12.1 - - + -
144A LEU* 3.9 29.8 - - + -
145A VAL 2.9 17.0 + - - +
146A ASP* 4.2 10.5 - - - +
147A LEU* 3.4 28.8 + - - +
182A LEU* 3.5 29.8 - - + +
184A VAL* 3.9 20.9 - - + -
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Residues in contact with VAL 31 (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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29A VAL* 3.5 4.7 + - + +
30A VAL* 1.3 76.7 - - - +
32A GLY* 1.3 55.8 + - - +
38A LYS* 4.4 1.3 - - - -
147A LEU* 4.6 3.6 - - + -
150A MET* 3.9 24.5 - - + -
170A ILE* 3.9 18.2 - - + -
174A ILE* 3.7 30.3 - - + -
181A ILE* 4.1 16.6 - - + -
182A LEU 2.8 11.2 + - - +
183A ALA* 3.3 3.0 - - - -
184A VAL* 2.7 33.0 + - - -
196A ALA* 3.8 15.1 - - - +
199A ILE* 4.0 11.7 - - + -
200A SER* 4.6 2.7 - - - +
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Residues in contact with GLY 32 (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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31A VAL* 1.3 75.7 - - - +
33A THR* 1.3 62.0 + - - -
36A SER* 3.8 4.0 - - - -
38A LYS* 3.6 25.2 - - - +
148A PRO 4.6 1.1 + - - +
149A GLY* 3.4 7.3 - - - -
150A MET* 3.2 27.8 + - - +
170A ILE* 5.4 0.9 - - - +
184A VAL* 3.7 13.7 - - - -
196A ALA* 4.3 1.6 - - - -
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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