Contacts of the strand formed by residues 211 - 215 (chain A) in PDB entry 3V56
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 211 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A TYR* 4.3 15.0 - - + +
210A HIS* 1.3 80.1 - - - +
212A ILE* 1.4 61.0 + - - +
213A GLN* 3.6 34.5 + - + +
228A THR* 3.7 14.4 - - + +
230A PHE 3.5 3.8 - - - -
231A ARG* 3.5 35.4 - - + -
260A GLN 3.3 2.3 - - - +
261A LEU* 3.3 6.0 - - - -
262A ALA* 2.8 37.3 + - + +
264A PRO* 3.8 26.2 - - + -
27G LEU* 5.3 2.5 - - + +
28G LEU* 4.1 4.0 - - + -
30G ARG* 4.4 8.5 - - - +
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Residues in contact with ILE 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A ILE* 3.6 25.6 - - + -
196A TYR* 3.8 9.4 - - - +
197A GLY* 3.7 29.6 - - - +
210A HIS* 4.3 13.9 - - + +
211A LEU* 1.4 70.6 - - - +
213A GLN* 1.3 57.8 + - - +
228A THR* 3.7 1.0 - - - -
229A LEU* 2.8 42.3 + - + +
230A PHE* 2.8 40.0 + - + +
247A SER* 3.8 13.7 - - - +
259A LEU* 5.0 1.8 - - + -
260A GLN 3.5 2.7 - - - +
261A LEU* 4.6 3.6 - - + -
279A PHE* 4.1 19.5 - - + -
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Residues in contact with GLN 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A TYR* 5.4 5.4 + - - -
211A LEU* 3.6 34.8 - - + +
212A ILE* 1.3 77.8 - - - +
214A ARG* 1.3 59.7 + - - +
215A LYS 4.1 0.2 - - - -
226A LEU* 3.5 29.0 - - + +
227A VAL 3.1 6.3 - - - +
228A THR* 3.4 22.5 + - - +
229A LEU* 4.7 0.9 - - - -
258A GLU 3.8 0.3 - - - +
259A LEU* 3.3 11.7 - - - +
260A GLN* 2.7 72.0 + - + +
262A ALA* 3.5 10.3 - - - +
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Residues in contact with ARG 214 (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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213A GLN* 1.3 73.5 - - - +
215A LYS* 1.3 60.2 + - - +
216A LYS* 3.4 29.7 + - - +
225A SER 3.3 5.7 - - - +
226A LEU* 3.3 3.6 - - - -
227A VAL* 2.9 40.8 + - + +
229A LEU* 3.9 24.7 - - + +
252A LYS* 3.8 18.8 + - - +
253A LEU* 3.7 21.9 - - + +
254A GLU* 3.5 23.6 + - - +
257A ASP* 2.8 34.9 + - + +
258A GLU 3.5 6.5 - - - +
259A LEU* 4.1 2.7 - - + -
220F PHE* 5.8 4.4 - - - +
223F GLU* 3.8 20.6 + - - -
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Residues in contact with LYS 215 (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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184A LYS* 6.5 0.2 - - + -
213A GLN 4.1 0.6 - - - -
214A ARG* 1.3 69.3 - - - +
216A LYS* 1.3 71.1 + - - +
217A VAL* 4.6 0.3 - - - -
225A SER* 3.6 29.2 - - - +
226A LEU* 3.8 21.0 - - + +
256A GLY 4.6 0.7 - - - +
257A ASP* 3.4 4.3 - - - -
258A GLU* 2.7 51.4 + - + +
260A GLN* 5.7 4.7 - - + +
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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