Contacts of the strand formed by residues 198 - 207 (chain A) in PDB entry 3OJW
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 GLN 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A GLY* 5.6 2.6 - - - +
166A VAL 2.6 15.1 + - - +
167A LYS* 3.3 27.8 - - + -
168A PHE* 2.9 26.5 + - - -
196A GLY 5.3 0.4 - - - +
197A ALA* 1.3 71.8 - - - +
199A ARG* 1.3 67.8 + - - +
200A ILE* 3.4 13.3 + - + +
230A PHE* 3.5 25.1 - - - -
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Residues in contact with ARG 199 (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 PHE* 3.5 25.4 - - + +
189A ASP* 2.8 50.0 + - - +
190A GLN* 4.6 2.0 - - - +
193A GLU* 2.8 37.3 + - + +
197A ALA 4.0 1.0 + - - -
198A GLN* 1.3 75.6 + - - +
200A ILE* 1.3 64.0 + - - +
201A PHE 3.2 30.1 - - - +
202A GLU* 4.2 8.3 - - - +
203A LEU 5.0 0.8 - - - +
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Residues in contact with ILE 200 (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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132A LEU* 4.6 12.3 - - + -
167A LYS* 3.8 14.6 - - + -
168A PHE 2.9 13.7 + - - +
169A ALA* 5.3 0.2 - - + -
198A GLN* 3.4 28.0 - - + +
199A ARG* 1.3 77.9 - - - +
201A PHE* 1.3 64.9 + - + +
223A PHE* 5.2 1.1 - - + -
226A ALA* 4.6 7.3 - - - +
227A VAL* 3.9 35.4 - - + +
230A PHE* 3.6 52.5 - - + -
231A PHE* 5.4 2.0 - - + -
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Residues in contact with PHE 201 (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 PHE 4.0 2.6 + - - -
169A ALA* 4.2 15.1 - - + -
170A VAL 4.7 0.3 + - - -
189A ASP* 5.0 0.3 - - - +
199A ARG* 3.2 19.5 - - - +
200A ILE* 1.3 82.2 - - + +
202A GLU* 1.3 91.6 + - + +
203A LEU* 3.6 0.7 + - - -
219A TRP* 3.3 45.3 - + - -
222A GLN* 3.5 42.4 - - + -
223A PHE* 3.7 35.7 - + + -
226A ALA* 3.7 20.6 - - + -
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Residues in contact with GLU 202 (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 VAL 3.9 1.9 - - - +
199A ARG* 4.2 8.9 - - - +
201A PHE* 1.3 103.8 - - + +
203A LEU* 1.3 69.7 + - - +
204A GLY 3.4 0.2 + - - -
219A TRP* 3.0 29.8 + - + +
222A GLN* 4.3 11.4 - - - +
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Residues in contact with LEU 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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170A VAL* 3.4 37.9 - - + +
172A GLY 4.2 1.8 - - - +
185A GLY* 3.8 11.2 - - - +
186A LYS* 3.8 35.9 - - + -
189A ASP* 3.9 29.7 + - + +
199A ARG* 4.7 1.8 - - - +
201A PHE 3.6 1.4 + - - -
202A GLU* 1.3 81.6 - - - +
204A GLY* 1.3 77.6 + - - +
205A LEU* 3.8 19.6 + - + +
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Residues in contact with GLY 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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170A VAL 2.8 12.9 + - - -
171A PHE* 3.8 11.0 - - - -
172A GLY* 2.8 26.2 + - - -
202A GLU 3.4 2.2 + - - -
203A LEU* 1.3 79.8 - - - +
205A LEU* 1.3 61.2 + - - +
206A GLY 3.8 2.0 - - - -
219A TRP* 3.4 25.8 - - - +
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Residues in contact with LEU 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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171A PHE* 4.6 2.1 - - - -
176A LYS* 5.0 2.1 + - - +
181A PHE* 4.2 20.3 - - + -
182A ASN* 3.7 30.5 - - + +
186A LYS* 4.0 18.8 - - + +
203A LEU* 3.8 30.9 + - + +
204A GLY* 1.3 78.8 - - - +
206A GLY* 1.3 64.9 + - - +
207A ASP* 3.5 3.5 + - - +
215A ASP* 4.0 7.4 - - - +
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Residues in contact with GLY 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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171A PHE* 3.9 11.4 - - - -
172A GLY 2.9 16.0 + - - -
174A GLY 3.1 14.4 + - - +
181A PHE* 3.7 1.0 - - - -
182A ASN* 2.9 17.3 - - - +
204A GLY 3.8 1.0 - - - -
205A LEU* 1.3 72.5 - - - +
207A ASP* 1.3 59.6 + - - -
212A LEU* 3.4 24.5 - - - -
215A ASP* 3.7 7.9 - - - -
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Residues in contact with ASP 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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174A GLY 3.6 1.6 - - - -
176A LYS* 3.2 55.5 + - - +
181A PHE* 4.1 5.2 - - + -
205A LEU 4.6 0.9 - - - +
206A GLY* 1.3 72.8 - - - -
208A ASP* 1.3 63.0 + - - +
209A ASP* 2.6 39.2 + - - +
210A GLY* 3.1 18.0 + - - -
211A ASN 3.4 12.6 + - - -
212A LEU* 3.4 7.5 + - - +
215A ASP* 2.8 15.6 + - - +
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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