Contacts of the strand formed by residues 202 - 211 (chain A) in PDB entry 2XXL
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 202 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A ILE 3.5 1.0 - - - +
176A ARG* 3.3 4.9 - - - +
177A LEU* 2.9 35.7 + - + +
200A PRO 4.6 2.2 - - - +
201A VAL* 1.3 75.8 - - - +
203A ASN* 1.3 63.3 - - - +
204A VAL* 4.2 6.5 - - + -
231A ARG* 3.8 21.1 - - - +
233A VAL* 3.9 26.0 - - + -
236A GLN* 4.2 18.2 - - - +
239A ILE* 3.5 27.3 - - + +
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Residues in contact with ASN 203 (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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137A ARG* 5.0 0.9 + - - -
146A PHE* 5.1 0.5 - - - -
174A GLU* 3.9 25.1 - - - +
175A ILE 3.4 4.3 - - - +
176A ARG* 2.8 43.3 + - - +
201A VAL* 3.8 19.6 + - - +
202A VAL* 1.3 70.6 - - - +
204A VAL* 1.3 58.5 + - - +
231A ARG* 3.3 16.7 + - - +
1C NAG 5.7 0.3 - - - -
2C NAG 4.6 17.4 - - + +
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Residues in contact with VAL 204 (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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174A GLU* 3.3 8.5 - - - +
175A ILE* 2.8 46.1 + - + +
177A LEU* 4.3 8.5 - - + -
202A VAL* 4.2 3.1 - - + -
203A ASN* 1.3 74.8 - - - +
205A GLY* 1.3 67.8 + - - +
229A LEU* 3.8 30.1 - - + -
230A ASN* 3.4 13.7 - - - +
231A ARG* 3.7 33.4 - - + +
233A VAL* 4.0 22.2 - - + -
1C NAG 4.6 0.7 - - - -
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Residues in contact with GLY 205 (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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173A TYR 3.7 6.1 - - - -
204A VAL* 1.3 76.4 - - - +
206A ILE* 1.3 63.8 + - - +
229A LEU* 3.4 9.0 - - - +
230A ASN* 3.0 37.0 + - - -
1C NAG 3.4 11.4 + - - -
4C FUC 3.2 20.6 - - - -
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Residues in contact with ILE 206 (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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172A LEU* 3.7 35.2 - - + +
173A TYR* 4.0 20.1 + - - +
175A ILE* 3.8 32.5 - - + -
205A GLY* 1.3 78.1 - - - +
207A GLU* 1.3 61.6 + - - +
208A LYS 3.3 25.6 - - - +
209A HIS* 3.7 28.9 - - + +
227A LEU* 4.2 14.6 - - + -
228A LYS 3.5 7.4 - - - +
229A LEU* 5.0 1.1 - - + -
4C FUC 3.6 21.5 + - - +
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Residues in contact with GLU 207 (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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156A ARG* 5.1 4.3 + - - -
206A ILE* 1.3 74.4 - - - +
208A LYS* 1.3 71.0 + - + +
209A HIS* 5.1 2.3 + - - -
228A LYS* 2.7 30.7 + - - +
229A LEU 3.9 3.2 - - - +
230A ASN* 3.9 24.1 - - + +
378A LEU 5.0 0.2 - - - +
379A GLU* 5.5 0.2 - - - -
380A SER* 2.7 38.4 + - - -
4C FUC 5.1 1.3 - - - -
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Residues in contact with LYS 208 (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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82A ASN* 5.2 1.2 + - - +
206A ILE* 3.3 10.6 - - - +
207A GLU* 1.3 95.4 - - + +
209A HIS* 1.3 61.1 + - - +
210A LEU* 3.8 17.5 + - + +
227A LEU* 3.5 2.4 - - - -
228A LYS* 2.9 38.3 + - + +
374A SER 5.1 0.8 + - - -
375A ASN* 3.0 49.5 + - + +
380A SER* 3.0 34.1 + - - +
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Residues in contact with HIS 209 (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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165A VAL* 3.6 24.7 - - + -
169A GLN* 3.6 51.9 + - + +
172A LEU* 3.1 30.8 + - + +
206A ILE* 3.7 26.4 - - + +
207A GLU 5.1 1.4 + - - -
208A LYS* 1.3 73.3 - - - +
210A LEU* 1.4 64.3 + - - +
211A ILE* 3.7 7.6 + - - +
226A LEU 4.1 2.2 - - - -
227A LEU* 3.9 14.8 - - + -
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Residues in contact with LEU 210 (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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157A TYR* 4.0 23.1 - - + -
165A VAL* 4.8 1.0 - - - +
208A LYS* 3.8 23.8 - - + +
209A HIS* 1.4 74.2 - - - +
211A ILE* 1.3 63.4 + - - +
225A ALA* 3.2 3.5 - - - -
226A LEU* 2.8 47.2 + - + +
228A LYS* 4.4 2.5 - - + -
367A TRP* 3.6 6.1 - - - -
371A THR* 4.0 22.0 - - + -
375A ASN* 3.5 42.6 - - + +
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Residues in contact with ILE 211 (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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162A ALA* 3.7 22.0 - - + +
165A VAL* 3.8 26.9 - - + -
166A HIS* 3.7 32.3 - - + +
169A GLN* 3.4 28.7 - - - +
209A HIS 3.7 5.8 + - - +
210A LEU* 1.3 73.4 - - - +
212A HIS* 1.4 79.3 + - - +
213A GLU* 3.3 8.3 + - - +
215A TYR* 3.7 14.8 - - + -
225A ALA* 4.0 6.1 - - + -
367A TRP* 4.0 3.6 - - - -
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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