Contacts of the strand formed by residues 211 - 215 (chain A) in PDB entry 4X8G
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 VAL 211 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A LEU* 4.2 4.5 - - + -
203A VAL* 4.4 12.3 - - + -
207A GLU 3.5 16.6 - - - +
208A MET* 3.1 23.7 - - - +
209A ASP 3.5 0.6 - - - -
210A LYS* 1.3 82.0 - - - +
212A ARG* 1.3 67.1 + - - +
213A VAL* 4.4 7.0 - - + -
229A LEU* 6.2 1.1 - - + -
230A GLY* 3.3 10.8 + - - +
231A PRO* 3.9 1.7 - - - +
251A VAL* 3.6 24.0 - - + -
252A GLU 3.3 14.1 - - - +
254A LEU* 3.8 4.7 - - - +
265A ILE* 3.8 31.0 - - + -
267A LEU* 4.7 4.0 - - + -
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Residues in contact with ARG 212 (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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166A CYS 3.3 21.0 + - - -
167A GLU 4.9 3.4 + - - -
168A ASP 2.9 28.5 + - - -
169A ASP* 3.9 17.0 - - - +
211A VAL* 1.3 75.1 - - - +
213A VAL* 1.3 66.4 + - - +
214A PHE* 3.6 21.9 + - + -
227A VAL* 4.2 9.3 - - + +
229A LEU 3.4 13.7 - - - +
230A GLY* 4.4 1.8 - - - -
231A PRO* 3.9 18.0 - - - +
250A TYR 4.0 0.7 - - - +
251A VAL* 3.8 1.2 - - - -
252A GLU* 3.0 68.6 + - + +
254A LEU* 3.3 26.9 - - + +
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Residues in contact with VAL 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A MET* 4.3 5.6 - - + -
201A LEU* 4.4 4.0 - - + -
211A VAL* 4.4 10.5 - - + -
212A ARG* 1.3 78.4 - - - +
214A PHE* 1.3 71.8 + - - +
227A VAL* 3.7 5.4 - - - +
228A VAL* 3.1 37.1 + - + -
229A LEU* 2.8 40.0 + - + +
249A PHE* 4.2 17.5 - - + -
250A TYR 3.6 6.1 - - - +
251A VAL* 4.2 10.5 - - + -
267A LEU* 4.1 24.9 - - + -
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Residues in contact with PHE 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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168A ASP 5.2 0.4 - - - -
170A GLU* 3.9 21.8 - - - -
171A VAL* 3.7 27.6 - - + -
180A MET* 3.8 17.0 - - + -
212A ARG* 3.6 16.8 - - + -
213A VAL* 1.3 75.4 - - - +
215A GLN* 1.3 60.1 + - - +
225A CYS* 4.4 13.7 - - + -
226A SER* 3.3 20.4 - - - +
227A VAL* 3.5 26.2 - - + -
228A VAL* 4.3 3.6 - - - -
249A PHE* 3.2 9.2 - - - +
250A TYR* 2.8 50.7 + - + +
252A GLU* 3.2 35.2 - - + -
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Residues in contact with GLN 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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214A PHE* 1.3 74.8 - - - +
216A ALA* 1.3 69.2 + - - +
217A THR* 4.0 7.5 + - - +
224A LYS 3.8 0.2 - - - +
225A CYS* 3.4 6.2 - - - -
226A SER* 2.8 42.2 + - - +
228A VAL* 3.7 21.9 - - + +
236A HIS* 6.0 0.2 - - - -
238A LEU* 4.7 5.3 - - - +
239A MET* 5.0 7.2 + - - +
247A MET* 3.0 37.1 - - + +
248A ASP 3.8 7.2 - - - +
249A PHE* 4.0 18.6 - - + -
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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
------------------------------------------------------------
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