Contacts of the strand formed by residues 222 - 231 (chain A) in PDB entry 2GP0
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 GLU 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A TRP* 3.4 21.9 - - + -
218A GLN* 3.2 3.9 - - - +
219A TYR 2.9 31.1 + - - +
221A GLU* 1.3 95.8 - - - +
223A ARG* 1.3 64.5 + - - +
224A ARG* 3.0 38.9 + - + +
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Residues in contact with ARG 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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200A ARG* 5.4 8.3 - - - +
216A THR* 3.7 36.2 - - + +
217A ILE 3.3 7.4 - - - +
218A GLN* 2.8 48.7 + - + +
221A GLU 3.9 2.9 + - - +
222A GLU* 1.3 77.9 - - - +
224A ARG* 1.3 65.8 + - - +
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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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162A VAL 4.4 0.6 + - - -
163A TRP* 2.7 76.3 + - + +
166A GLU* 3.7 32.1 + - - +
167A VAL 5.8 4.0 - - - +
216A THR* 3.2 6.2 - - - -
217A ILE* 2.8 41.8 + - + +
222A GLU* 3.0 30.3 + - + +
223A ARG* 1.3 78.6 - - - +
225A ASP* 1.3 69.6 + - - +
226A VAL* 5.4 0.7 - - + -
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Residues in contact with ASP 225 (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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167A VAL 4.5 0.7 - - - +
168A SER* 3.7 18.6 - - - -
214A GLN* 5.0 9.6 - - - +
215A LEU 3.5 5.4 - - - +
216A THR* 3.5 19.4 - - - +
224A ARG* 1.3 77.6 - - - +
226A VAL* 1.3 64.1 + - - +
227A LYS 4.3 0.2 - - - -
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Residues in contact with VAL 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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159A TRP* 5.0 4.0 - - + -
162A VAL* 4.3 7.6 - - + -
167A VAL* 3.7 17.0 - - + +
168A SER* 3.3 15.5 - - - +
170A ILE* 3.8 28.3 - - + -
214A GLN* 4.0 4.3 - - - +
215A LEU* 2.9 49.9 + - + +
216A THR 5.4 0.2 - - - -
217A ILE* 3.9 28.3 - - + +
224A ARG* 3.8 0.9 + - + +
225A ASP* 1.3 78.0 - - - +
227A LYS* 1.3 71.6 + - - +
228A HIS 3.8 0.3 + - - -
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Residues in contact with LYS 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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168A SER 2.6 15.3 + - - +
169A LEU* 3.3 13.5 - - + +
170A ILE 2.9 25.1 + - - -
212A VAL* 3.7 22.0 - - + -
213A ARG 3.6 3.8 - - - +
214A GLN* 3.7 27.5 + - - +
225A ASP 4.3 0.2 - - - -
226A VAL* 1.3 74.6 - - - +
228A HIS* 1.3 60.8 + - - +
229A ILE* 4.1 11.7 - - + -
252A GLU* 2.7 36.1 + - - -
255A GLU* 4.1 4.4 - - - +
256A SER* 2.7 40.9 + - - +
257A PRO* 4.6 9.9 - - + +
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Residues in contact with HIS 228 (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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170A ILE* 3.4 25.8 - - + -
172A MET* 3.9 29.6 - - + +
186A TYR* 2.7 37.5 + + - -
187A TRP* 3.9 17.3 - + - -
211A THR 3.6 1.2 - - - +
212A VAL* 3.4 4.3 - - - +
213A ARG* 2.7 59.6 + - + +
215A LEU* 4.1 22.4 - - + -
226A VAL 3.8 0.4 + - - -
227A LYS* 1.3 74.6 - - - +
229A ILE* 1.3 63.0 + - - +
230A LEU* 4.1 13.4 + - + +
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Residues in contact with ILE 229 (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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169A LEU* 3.8 26.2 - - + -
170A ILE 2.8 12.2 + - - +
171A VAL* 3.7 4.5 - - + +
172A MET* 2.8 31.4 + - - +
210A TYR* 3.7 29.8 - - + -
211A THR 3.5 3.4 - - - +
212A VAL* 4.4 3.4 - - + -
227A LYS* 4.1 12.6 - - - -
228A HIS* 1.3 80.1 - - - +
230A LEU* 1.3 61.7 + - - +
231A PHE 3.8 0.3 + - - -
249A LEU* 3.5 25.4 - - + -
252A GLU* 3.5 25.4 - - + -
253A VAL* 4.0 21.8 - - + +
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Residues in contact with LEU 230 (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 MET* 3.6 23.8 - - + -
174A THR* 3.6 23.8 - - + -
187A TRP* 3.7 31.0 - - + -
210A TYR* 3.2 5.4 - - - +
211A THR* 2.9 42.8 + - - +
213A ARG* 3.9 21.1 - - - +
228A HIS* 4.1 6.9 - - + -
229A ILE* 1.3 73.2 - - - +
231A PHE* 1.3 59.5 + - - +
232A SER* 3.9 16.3 + - - +
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Residues in contact with PHE 231 (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 MET 2.9 14.4 + - - +
173A LEU* 4.0 2.7 - - + -
174A THR* 3.0 24.4 + - - +
209A GLU* 3.6 18.6 - - + -
210A TYR* 4.0 10.5 - + + -
229A ILE 3.8 0.8 + - - +
230A LEU* 1.3 72.7 - - - +
232A SER* 1.3 73.9 + - - +
233A ALA* 4.6 3.4 - - + -
234A TRP* 3.8 37.2 - + + -
240A PRO* 4.5 15.0 - - + -
245A PRO* 3.5 43.3 - - + -
246A LEU* 4.4 6.3 - - + -
249A LEU* 3.7 37.5 - - + -
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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