Contacts of the strand formed by residues 159 - 168 (chain B) in PDB entry 2COJ
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 SER 159 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B LYS* 3.2 35.5 + - - +
100B ALA 3.5 14.1 - - - -
101B PHE* 3.8 22.0 - - - +
152B VAL* 5.4 0.4 - - - -
153B PRO* 3.4 19.1 - - - +
158B ALA* 1.3 77.1 - - - +
160B LEU* 1.3 61.4 + - - +
161B TYR 4.0 0.2 - - - -
189B PRO* 3.5 1.4 - - - +
190B VAL* 2.9 32.3 + - - +
191B GLY 5.3 0.3 + - - -
374B TYR* 4.5 0.2 - - - -
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Residues in contact with LEU 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B THR* 4.1 7.4 - - + -
99B LYS* 3.3 5.6 - - - -
100B ALA* 3.0 36.3 + - + +
145B VAL* 4.6 9.0 - - + -
148B ASP 4.9 1.8 - - - +
151B TRP* 4.0 12.8 - - + +
152B VAL* 3.7 35.7 - - + +
153B PRO* 4.0 0.2 - - - +
159B SER* 1.3 76.3 - - - +
161B TYR* 1.3 69.5 + - - +
162B ILE* 3.6 3.0 + - + +
187B LEU* 4.0 29.2 - - + -
188B SER 3.5 8.3 - - - +
189B PRO* 3.3 38.4 - - + -
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Residues in contact with TYR 161 (chain B).
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* 3.8 22.2 - - + -
49B PHE* 3.7 31.6 - + - -
95B PHE* 5.1 0.7 - - - -
96B GLU 4.0 0.2 + - - -
97B GLY* 3.5 29.6 - - - -
98B LEU 3.8 7.0 - - - -
99B LYS* 4.3 17.0 - - + -
159B SER 4.0 1.6 + - - -
160B LEU* 1.3 73.5 - - - +
162B ILE* 1.3 66.5 + - - +
163B ARG* 2.8 44.5 + - + -
186B LEU 3.7 0.7 - - - +
187B LEU* 3.4 5.4 - - - +
188B SER* 2.8 45.3 + - - +
190B VAL* 3.8 14.3 - - + +
222B LYS* 5.8 0.2 - - - -
333B THR* 4.7 7.9 - - + -
334B ALA* 5.2 0.7 - - + -
420B GBN 3.4 20.7 + - - +
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Residues in contact with ILE 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B GLY* 3.8 4.5 - - - -
98B LEU* 2.6 66.7 + - + +
99B LYS 4.3 0.9 - - - -
100B ALA* 4.2 7.4 - - + -
110B LEU* 3.9 19.1 - - + -
141B ILE* 4.0 13.2 - - + -
145B VAL* 3.7 22.9 - - + -
160B LEU* 3.8 7.6 - - + +
161B TYR* 1.3 78.4 - - - +
163B ARG* 1.3 61.9 + - - +
164B PRO* 3.2 8.2 - - + +
185B VAL* 3.6 24.0 - - + -
186B LEU 3.6 2.5 - - - -
187B LEU* 3.6 16.2 - - + -
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Residues in contact with ARG 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A HIS* 3.1 25.1 + - + +
90A TYR* 3.0 33.1 + - - -
173A LEU* 3.4 30.6 - - + +
95B PHE* 3.6 20.0 - - - -
96B GLU 2.8 20.6 + - - -
161B TYR* 2.8 37.3 + - + -
162B ILE* 1.3 74.6 - - - +
164B PRO* 1.3 69.4 - - - +
165B THR* 3.4 16.1 + - - +
185B VAL* 3.3 3.1 - - - -
186B LEU* 2.7 41.5 + - + +
420B GBN 3.5 14.6 - - - +
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Residues in contact with PRO 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B PHE* 3.4 3.1 - - - -
96B GLU* 3.0 38.0 + - + +
98B LEU* 3.5 18.6 - - + -
117B MET* 4.8 3.8 - - + -
120B MET* 3.7 27.8 - - + -
137B LEU* 5.2 1.6 - - + -
141B ILE* 3.7 26.7 - - + -
162B ILE* 3.2 12.6 - - + +
163B ARG* 1.3 88.3 - - - +
165B THR* 1.3 60.5 + - - +
183B LEU* 5.2 0.2 - - + -
184B PHE 3.4 5.8 - - - +
185B VAL* 3.9 12.3 - - + -
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Residues in contact with THR 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A LEU 4.0 16.2 - - - +
89A HIS* 3.2 32.4 - - + +
94B LEU 3.7 10.5 - - - +
95B PHE* 4.5 2.9 - - + -
120B MET* 4.1 1.4 - - - +
163B ARG* 3.4 11.8 + - - +
164B PRO* 1.3 77.2 + - - +
166B PHE* 1.3 63.0 + - - +
167B ILE* 4.4 3.1 - - + -
183B LEU* 3.1 6.1 - - - +
184B PHE* 2.6 71.0 + - + -
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Residues in contact with PHE 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B TRP* 3.6 20.4 - + - -
93B GLU* 3.2 5.2 - - - -
94B LEU* 3.0 47.4 + - + +
120B MET* 4.2 11.7 - - + -
124B ALA* 4.1 12.1 - - + -
129B LEU* 3.7 18.3 - - + +
130B PRO* 3.1 55.4 - - + -
132B PHE* 3.7 26.9 - + - -
165B THR* 1.3 74.0 - - - +
167B ILE* 1.3 62.6 + - - +
181B ALA* 4.2 7.9 - - + -
182B LEU 3.5 13.0 - - - -
183B LEU* 4.0 12.1 - - + -
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Residues in contact with ILE 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A LEU* 3.9 52.0 - - + +
79B LEU* 4.6 1.8 - - + -
81B LEU* 4.1 16.2 - - + -
85B SER* 6.2 0.2 - - - -
87B ALA* 3.7 10.5 - - + -
92B VAL 3.7 2.9 - - - -
93B GLU* 4.0 5.4 - - + -
129B LEU* 4.2 4.7 - - - -
165B THR* 4.2 2.7 - - + -
166B PHE* 1.3 78.6 - - - +
168B GLY* 1.3 60.3 + - - +
169B THR* 4.0 17.7 - - + -
181B ALA* 3.3 3.8 - - - +
182B LEU* 2.9 58.3 + - + +
184B PHE* 4.1 23.3 - - + -
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Residues in contact with GLY 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B SER* 3.8 1.2 - - - -
86B SER* 3.5 13.9 + - - -
87B ALA* 3.0 29.3 + - - +
92B VAL* 2.9 24.2 + - - -
129B LEU* 4.1 9.7 - - - +
167B ILE* 1.3 72.1 - - - +
169B THR* 1.3 61.5 + - - +
170B GLU 3.5 3.1 - - - -
178B PRO* 4.4 3.1 - - - -
180B LYS 3.8 5.8 - - - -
181B ALA* 4.3 0.2 - - - -
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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