Contacts of the strand formed by residues 208 - 214 (chain A) in PDB entry 5GKI
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 208 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A ASN* 4.4 1.4 + - - +
175A ILE* 3.2 19.3 - - + +
177A VAL* 4.2 10.3 - - + -
197A VAL* 4.1 15.3 - - + -
200A LEU* 3.7 37.7 - - + +
201A ARG* 3.2 35.2 + - + +
204A TYR* 4.4 6.5 - - + -
205A GLY 3.5 17.0 - - - +
206A ASP 3.3 3.4 + - - +
207A LYS* 1.3 81.4 - - - +
209A ARG* 1.3 75.2 + - - +
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Residues in contact with ARG 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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147A GLU* 2.7 41.2 + - - -
170A ASP* 2.6 43.5 + - - +
174A ASN* 4.1 16.4 - - + +
175A ILE 2.7 8.8 + - - +
176A VAL* 3.3 12.3 - - + +
177A VAL* 2.7 34.8 + - - +
201A ARG* 5.3 0.2 - - - +
208A VAL* 1.3 83.2 - - - +
210A GLY* 1.3 55.8 + - - +
211A ILE* 3.8 11.4 - - + +
231A GLU* 2.7 45.2 + - + +
233A ARG* 4.2 1.0 - - - +
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Residues in contact with GLY 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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177A VAL* 3.4 5.8 - - - -
193A LEU* 3.7 7.0 - - - -
197A VAL* 3.6 16.2 - - - +
201A ARG* 5.6 0.4 - - - +
209A ARG* 1.3 73.8 - - - +
211A ILE* 1.3 65.1 + - - +
230A LEU* 3.5 28.9 - - - +
231A GLU* 3.2 25.5 + - - +
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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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146A ILE* 4.3 15.0 - - + -
147A GLU* 4.5 4.3 - - - +
176A VAL* 3.8 25.4 - - + -
177A VAL 2.7 9.1 + - - -
178A LEU* 3.3 18.2 - - + +
179A GLU 3.0 22.3 + - - -
193A LEU* 3.7 3.9 - - - +
209A ARG* 3.8 23.3 - - + +
210A GLY* 1.3 79.3 - - - +
212A LEU* 1.3 71.0 + - - +
213A VAL* 3.6 11.1 + - + -
231A GLU* 3.2 26.9 - - + +
232A PHE 4.2 0.2 - - - +
233A ARG* 3.9 25.1 - - + +
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Residues in contact with LEU 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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179A GLU* 3.2 33.9 - - + +
181A LYS* 4.5 3.1 - - + -
185A ALA* 3.7 20.9 - - + -
189A ALA* 4.5 7.4 - - + -
190A VAL* 3.8 27.6 - - + +
193A LEU* 3.5 14.9 - - + +
211A ILE* 1.3 70.8 - - - +
213A VAL* 1.3 70.0 + - - +
214A ALA* 4.5 0.9 - - + -
217A LEU* 3.6 31.0 - - + -
225A LEU* 4.3 9.0 - - + -
231A GLU 2.7 14.3 + - - +
232A PHE* 3.3 7.9 - - + -
233A ARG 2.9 23.6 + - - -
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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
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135A MET* 4.0 4.1 - - + +
139A ILE* 4.7 0.4 - - + -
146A ILE* 3.8 27.8 - - + -
178A LEU* 4.2 7.6 - - + -
179A GLU 2.7 9.5 + - - +
180A LEU* 3.2 24.9 - - + +
181A LYS 3.0 24.6 + - - +
211A ILE* 4.0 20.9 - - + +
212A LEU* 1.3 77.2 - - - +
214A ALA* 1.3 63.5 + - - +
233A ARG* 3.3 10.8 - - + +
235A LEU* 3.5 34.8 - - + -
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Residues in contact with ALA 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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135A MET* 4.5 0.2 - - - -
181A LYS* 3.3 24.2 - - + +
183A ARG 3.7 9.2 - - - +
185A ALA* 4.1 8.3 - - + -
212A LEU* 4.1 4.1 + - + -
213A VAL* 1.3 78.3 - - - +
215A PRO* 1.3 73.3 - - + +
216A SER 3.2 11.2 - - - +
232A PHE* 3.3 8.9 - - + -
233A ARG 3.3 4.0 + - - -
234A LYS* 3.1 8.8 - - - -
235A LEU 2.9 21.4 + - - -
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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