Contacts of the strand formed by residues 222 - 227 (chain A) in PDB entry 4BN4
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 LEU 222 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A GLN 5.4 0.4 - - - -
140A VAL* 3.6 15.7 - - - +
142A VAL* 3.7 20.9 - - + -
213A LEU* 4.3 10.1 - - + +
216A LEU* 3.7 12.1 + - + -
217A HIS* 3.8 36.5 - - + +
220A GLY 3.6 2.3 - - - -
221A LEU* 1.3 75.8 - - - +
223A LEU* 1.3 52.2 + - - +
224A ARG* 3.7 20.4 - - - +
225A LEU* 4.3 18.6 - - + +
239A ILE* 4.4 10.3 - - + -
243A LYS* 2.7 51.3 + - + -
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Residues in contact with LEU 223 (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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138A GLN 5.8 0.2 - - - -
139A ARG* 3.8 28.0 - - + +
140A VAL 2.8 16.8 + - - +
141A VAL* 3.7 11.7 - - + -
221A LEU 3.6 2.8 + - - -
222A LEU* 1.3 73.9 - - - +
224A ARG* 1.3 78.5 + - - +
243A LYS* 3.6 17.0 + - - +
308A ASP* 3.6 44.0 - - - +
311A MET* 4.1 17.0 - - + -
312A ALA* 4.2 4.7 - - - +
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Residues in contact with ARG 224 (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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140A VAL 3.5 0.8 + - - -
141A VAL* 3.4 6.5 - - + +
142A VAL 3.0 24.9 + - - +
222A LEU* 3.5 9.0 - - - +
223A LEU* 1.3 96.1 + - + +
225A LEU* 1.3 62.1 + - - +
226A TYR* 3.7 17.9 - - + -
242A SER* 2.8 29.7 + - - -
243A LYS* 3.4 25.1 - - - +
244A LEU 4.3 0.7 - - - +
245A VAL* 3.9 17.9 - - + -
301A ARG* 4.3 1.6 - - - +
304A LEU* 3.9 24.5 - - - +
307A VAL* 6.0 0.4 - - - +
308A ASP* 2.7 48.1 + - + +
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Residues in contact with LEU 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A VAL* 3.5 33.2 - - + +
144A VAL* 3.9 14.1 - - + -
213A LEU* 3.8 21.8 - - + -
222A LEU* 4.3 12.3 - - + -
224A ARG* 1.3 73.6 - - - +
226A TYR* 1.3 63.3 + - - +
234A GLU* 3.7 31.2 - - + -
239A ILE* 4.0 22.0 - - + -
243A LYS 2.9 13.7 + - - +
244A LEU* 3.4 15.4 - - + +
245A VAL 2.8 30.7 + - - -
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Residues in contact with TYR 226 (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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141A VAL* 4.0 14.6 - - + -
142A VAL 2.8 13.1 + - - +
143A MET* 3.3 7.5 - - + -
144A VAL* 3.0 25.8 + - - +
224A ARG* 3.7 12.8 - - + -
225A LEU* 1.3 75.6 - - - +
227A THR* 1.3 59.4 + - - +
245A VAL* 3.6 34.3 - - + -
302A PHE* 4.5 15.3 - + - -
304A LEU* 3.1 4.5 - - - +
305A HIS* 3.0 43.6 + - + -
308A ASP* 2.6 30.2 + - + -
309A PHE* 3.7 23.8 - + - -
327A PHE* 3.6 19.3 - + + -
330A LEU* 4.9 1.8 - - + -
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Residues in contact with THR 227 (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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144A VAL* 3.3 14.4 - - - +
225A LEU* 5.2 0.2 - - - -
226A TYR* 1.3 75.6 - - - +
228A GLN* 1.3 58.2 + - - +
229A ASN* 3.0 23.4 + - - +
234A GLU* 2.6 44.1 + - - +
244A LEU* 4.0 10.5 - - + -
245A VAL 2.9 17.3 + - - +
246A GLU* 3.8 15.2 - - + -
247A ALA* 2.9 31.4 + - - +
248A HIS 3.9 0.2 + - - -
327A PHE* 3.8 4.3 - - - -
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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