Contacts of the strand formed by residues 156 - 161 (chain B) in PDB entry 2CGA
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 156 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A GLU* 5.3 11.2 + - - +
18B ASN 4.7 5.9 - - - +
19B GLY 5.0 0.2 - - - -
20B GLU* 3.1 25.1 + - - +
21B GLU* 3.2 14.3 + - - +
22B ALA* 4.5 0.9 - - - -
139B THR* 3.3 7.2 - - - -
140B GLY 3.1 36.2 + - - +
141B TRP* 6.0 0.9 - - - -
143B LEU* 4.0 24.0 - - + +
154B ARG* 2.8 35.6 + - - +
155B LEU* 1.3 80.9 + - - +
157B GLN* 1.3 61.0 - - - +
192B MET* 4.0 15.7 - - + -
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Residues in contact with GLN 157 (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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8B PRO* 4.7 2.9 - - - +
9B VAL 2.8 29.0 + - - +
10B LEU* 3.7 16.7 - - + +
14B SER* 4.3 0.2 - - - -
18B ASN 4.8 0.2 - - - +
19B GLY* 3.4 0.9 - - - -
20B GLU* 2.8 67.3 + - + +
21B GLU 4.1 4.8 + - - -
22B ALA* 3.5 16.2 - - + +
23B VAL 4.7 1.0 + - - -
26B SER* 4.7 0.2 + - - -
27B TRP* 3.0 34.9 + - - +
137B VAL* 4.6 5.2 - - + -
138B THR 3.4 6.7 - - - -
139B THR* 4.1 5.2 - - + -
156B GLN* 1.3 74.0 - - - +
158B ALA* 1.3 63.9 + - - +
192B MET* 4.5 3.1 - - - -
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Residues in contact with ALA 158 (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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10B LEU* 5.2 0.7 - - - -
14B SER* 3.4 13.5 - - - +
19B GLY* 4.1 5.2 - - - -
137B VAL* 3.1 9.0 - - - +
138B THR* 2.9 37.2 + - + +
157B GLN* 1.3 77.1 - - - +
159B SER* 1.4 62.3 + - - +
160B LEU* 3.7 4.8 - - + +
188B VAL* 4.1 10.3 - - + -
189B SER 4.6 1.1 - - - +
192B MET* 3.5 31.9 - - + -
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Residues in contact with SER 159 (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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10B LEU* 3.6 17.5 - - - +
14B SER* 2.8 39.5 + - - +
15B ARG* 3.9 22.5 - - - +
135B THR* 3.9 19.0 - - - +
136B CYS 3.4 5.6 - - - -
137B VAL* 4.5 4.0 - - - +
158B ALA* 1.4 68.2 - - - +
160B LEU* 1.3 63.4 + - - +
161B PRO* 4.9 0.2 - - - +
186B SER* 4.9 1.7 + - - -
188B VAL* 3.9 11.3 - - - +
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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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135B THR* 4.0 5.0 - - - +
136B CYS* 2.8 56.2 + - - +
138B THR* 3.7 20.4 - - + +
158B ALA* 3.7 15.7 - - + +
159B SER* 1.3 75.1 - - - +
161B PRO* 1.3 69.8 - - + +
162B LEU 3.9 0.2 + - - -
183B ALA* 3.7 30.2 - - + +
184B GLY* 4.0 8.7 - - - +
188B VAL* 4.3 11.4 - - + -
189B SER 5.3 2.7 - - - +
190B SER* 4.3 13.5 - - - -
199B LEU* 3.8 13.0 - - + -
228B TYR* 3.7 21.8 - - - +
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Residues in contact with PRO 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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133B GLY* 4.5 13.2 - - - +
134B THR 3.3 9.6 - - - +
135B THR* 4.3 5.3 - - - +
160B LEU* 1.3 89.1 - - + +
162B LEU* 1.3 70.1 + - - +
163B LEU* 3.6 5.3 + - + +
183B ALA* 3.4 4.3 - - - -
184B GLY 3.0 32.4 + - - +
186B SER* 3.6 31.4 - - - +
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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