Contacts of the strand formed by residues 167 - 174 (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 LYS 167 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A LEU* 5.2 1.5 - - - +
131A SER 3.6 22.8 + - - +
132A LEU* 3.7 10.8 - - + +
133A VAL* 3.0 30.1 + - - +
165A GLY* 3.0 27.1 + - - +
166A VAL* 1.3 75.4 - - - +
168A PHE* 1.3 60.2 + - - +
198A GLN* 3.3 32.1 - - + +
200A ILE* 3.8 22.2 - - + -
230A PHE* 3.6 24.5 - - + -
231A PHE* 4.5 4.4 - - + -
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Residues in contact with PHE 168 (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* 3.8 5.1 - - - +
133A VAL* 3.1 21.8 - - + +
135A PHE* 4.6 1.1 - - + -
166A VAL* 5.0 1.8 - - + -
167A LYS* 1.3 76.2 - - - +
169A ALA* 1.3 65.3 + - - +
170A VAL* 3.8 8.3 - - + -
189A ASP* 3.5 48.7 - - - -
192A LEU* 3.5 34.5 - - + -
193A GLU* 4.0 5.6 - - - -
197A ALA* 3.7 25.4 - - + -
198A GLN 2.9 16.9 + - - -
199A ARG* 3.5 37.7 - - + +
200A ILE* 2.9 26.2 + - - +
201A PHE 4.0 0.3 + - - -
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Residues in contact with ALA 169 (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* 4.8 2.2 - - + -
133A VAL 3.3 3.9 + - - +
134A VAL* 3.3 13.6 - - + +
135A PHE* 3.0 24.4 + - - -
168A PHE* 1.3 80.3 - - - +
170A VAL* 1.3 66.6 + - - +
200A ILE* 5.3 0.7 - - + -
201A PHE* 4.2 20.9 - - + +
219A TRP* 4.3 4.9 - - + -
223A PHE* 3.6 31.9 - - + -
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Residues in contact with VAL 170 (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 PHE* 3.4 18.6 - - + +
137A MET* 4.9 4.3 - - + -
168A PHE* 3.8 19.1 - - + -
169A ALA* 1.3 82.4 - - - +
171A PHE* 1.3 68.0 + - - +
185A GLY* 3.7 18.8 - - - +
188A VAL* 4.2 12.3 - - + -
189A ASP* 4.0 24.3 + - + +
201A PHE 4.7 4.0 + - - -
202A GLU 4.9 0.2 + - - -
203A LEU* 3.4 28.2 - - + +
204A GLY 2.8 22.9 + - - -
219A TRP* 3.7 8.6 - - - -
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Residues in contact with PHE 171 (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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94A PHE* 4.0 28.3 - + + -
98A LEU* 5.4 3.4 - - + -
134A VAL* 5.8 0.2 - - + -
135A PHE 2.8 11.6 + - - +
136A ALA* 3.3 10.7 - - + -
137A MET 3.1 22.0 + - - -
170A VAL* 1.3 76.3 - - - +
172A GLY* 1.3 68.2 + - - +
173A LEU* 3.9 12.7 - - + +
204A GLY* 3.8 13.7 - - - -
205A LEU 4.6 0.7 - - - -
206A GLY* 3.9 21.3 - - - -
212A LEU* 4.3 4.0 - - + -
215A ASP* 3.9 3.8 - - + -
216A PHE* 3.5 39.0 - + + -
219A TRP* 3.5 50.2 - + + -
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Residues in contact with GLY 172 (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 MET 3.4 7.9 - - - -
170A VAL 4.1 1.0 - - - -
171A PHE* 1.3 77.7 - - - +
173A LEU* 1.3 59.6 + - - -
182A ASN* 2.8 18.1 + - - -
185A GLY* 4.2 13.9 - - - -
203A LEU* 4.2 3.0 - - - +
204A GLY 2.8 15.9 + - - -
206A GLY* 2.9 28.6 + - - -
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Residues in contact with LEU 173 (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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90A THR* 3.5 24.2 - - + -
91A ALA* 3.4 48.7 - - + +
94A PHE* 3.8 17.5 - - + -
136A ALA* 4.1 2.5 - - - -
137A MET 2.8 25.3 + - - +
138A ALA* 3.3 4.0 - - - -
139A THR* 3.1 25.3 + - - -
171A PHE* 3.9 16.2 - - + +
172A GLY* 1.3 71.9 - - - -
174A GLY* 1.3 58.4 + - - +
182A ASN* 3.0 7.8 + - - -
206A GLY 4.3 1.1 - - - -
212A LEU* 3.8 8.1 - - + -
751A FMN 3.4 21.6 + - - +
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Residues in contact with GLY 174 (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 LEU* 1.3 74.5 - - - +
175A ASN* 1.3 55.1 + - - -
181A PHE* 3.9 0.2 - - - -
182A ASN* 3.3 8.0 - - - +
206A GLY 3.1 17.2 + - - +
208A ASP* 2.7 36.9 + - - +
212A LEU* 4.9 1.1 - - - +
751A FMN 3.2 26.2 + - - -
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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