Contacts of the strand formed by residues 30 - 35 (chain A) in PDB entry 3H4B
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 ILE 30 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A ARG* 3.8 23.8 - - + +
29A VAL* 1.3 82.1 - - - +
31A VAL* 1.3 70.8 + - - +
129A PHE* 4.2 9.0 - - + -
130A VAL 3.6 8.1 - - - +
131A ASP* 3.7 31.4 - - + +
132A LEU* 4.8 0.9 - - - -
198A GLY 3.7 0.2 - - - +
199A VAL* 3.3 6.6 - - - +
200A ALA 2.7 34.7 + - - +
201A SER 4.0 3.1 - - - -
202A ASN* 3.8 32.5 - - - +
203A LYS* 4.2 25.1 - - + +
206A ALA* 4.3 2.7 - - + -
293A VAL* 4.1 7.9 - - + -
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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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30A ILE* 1.3 80.0 - - - +
32A HIS* 1.3 65.4 + - - +
33A VAL* 4.0 7.4 + - + -
128A ASN 3.7 1.2 - - - +
129A PHE* 3.3 6.9 - - - -
130A VAL* 3.0 57.2 + - + +
132A LEU* 3.4 25.8 - - + -
180A ALA* 4.1 16.4 - - + -
183A MET* 4.3 7.9 - - - -
197A ALA* 4.3 11.2 - - + -
198A GLY 3.1 11.2 - - - +
199A VAL* 4.1 13.0 - - + -
206A ALA* 4.3 0.2 - - - -
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Residues in contact with HIS 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 73.2 - - - +
33A VAL* 1.3 63.4 + - - +
34A ASP* 3.6 22.9 - - + -
127A GLU* 2.9 33.7 + - + +
128A ASN 3.6 7.6 - - - -
129A PHE* 3.5 31.4 - + + -
197A ALA* 3.1 4.7 - - - -
198A GLY 2.8 33.7 + - - -
206A ALA* 3.4 25.8 - - + +
207A LYS* 3.5 21.4 - - + +
210A SER* 2.6 31.5 + - - -
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Residues in contact with VAL 33 (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* 4.4 18.4 - - + -
32A HIS* 1.3 76.3 + - - +
34A ASP* 1.3 61.5 + - - +
35A LEU* 4.0 13.0 - - + -
109A VAL* 5.4 0.2 - - + -
113A LEU* 4.0 31.0 - - + -
126A ASP 3.8 0.7 - - - +
127A GLU* 3.4 6.9 - - - +
128A ASN* 2.9 39.5 + - + +
130A VAL* 5.1 0.7 - - + -
183A MET* 4.8 7.2 - - + -
184A ARG* 5.5 0.2 - - + -
187A MET* 3.6 36.3 - - + -
195A GLY* 5.8 0.7 - - - -
196A CYS 3.4 11.7 - - - +
197A ALA* 4.9 4.3 - - + -
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Residues in contact with ASP 34 (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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32A HIS* 3.6 22.5 + - + +
33A VAL* 1.3 73.0 - - - +
35A LEU* 1.3 76.4 + - - +
36A ASP* 3.6 2.4 + - - +
126A ASP* 3.6 8.4 - - - +
127A GLU* 3.9 20.6 - - + +
196A CYS* 2.9 42.2 + - + +
207A LYS* 5.6 0.2 + - - -
210A SER* 4.5 6.2 + - - +
211A GLY* 6.1 1.0 - - - -
214A LYS* 5.0 9.9 + - - -
875A DTP 4.1 16.0 + - - -
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Residues in contact with LEU 35 (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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33A VAL* 4.0 21.3 - - + +
34A ASP* 1.3 86.3 + - - +
36A ASP* 1.3 65.2 + - - +
37A CYS 3.6 2.3 + - - -
38A PHE* 3.3 44.9 + - + -
41A GLN* 4.6 0.9 - - - +
109A VAL* 4.0 22.0 - - + -
125A PHE 5.8 0.2 - - - +
126A ASP* 3.1 28.4 + - + +
128A ASN* 5.3 1.8 - - - +
187A MET* 4.5 5.4 - - - -
193A LEU* 3.8 26.2 - - + -
194A THR 4.0 10.5 - - - +
195A GLY* 4.1 5.2 - - - -
875A DTP 4.2 4.9 + - - -
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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
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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