Contacts of the strand formed by residues 183 - 187 (chain A) in PDB entry 2CNW
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 LEU 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A LEU* 4.2 3.1 - - + -
99A ASN* 3.4 20.4 - - + +
101A TRP* 3.8 31.6 - - + +
122A TYR* 3.3 48.0 - - + -
127A ARG* 4.0 15.7 - - + -
128A ARG 3.7 2.0 + - - -
129A PRO* 3.0 12.8 - - + +
130A LEU 2.6 33.7 + - - +
181A ARG 3.7 0.6 - - - -
182A ASP* 1.3 82.2 + - - +
184A ILE* 1.3 57.9 + - - +
185A LEU* 3.8 24.2 + - + -
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Residues in contact with ILE 184 (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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98A ARG* 5.8 7.0 - - + +
99A ASN 2.7 17.7 + - - +
100A LEU* 3.4 25.1 - - + -
101A TRP* 2.8 31.2 + - - +
130A LEU* 3.4 13.2 - - + +
132A VAL* 3.8 25.4 - - + -
172A VAL* 3.6 29.8 - - + -
173A GLU* 5.8 0.9 - - - -
176A ALA* 3.8 24.9 - - + -
181A ARG 4.8 4.7 - - - +
182A ASP 5.3 0.4 - - - -
183A LEU* 1.3 77.1 - - - +
185A LEU* 1.3 64.7 + - - +
186A VAL* 4.1 5.2 - - + -
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Residues in contact with LEU 185 (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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101A TRP* 3.8 33.9 - - + -
103A LEU* 4.6 11.4 - - + -
115A ALA* 3.8 7.6 - - + +
118A LEU* 4.1 18.8 - - + -
119A ALA* 3.6 38.8 - - + +
129A PRO* 4.0 15.3 - - + -
130A LEU 2.7 12.7 + - - +
131A LEU* 3.7 14.9 - - + +
132A VAL* 2.8 26.8 + - - -
183A LEU* 4.1 16.8 - - + +
184A ILE* 1.3 74.0 - - - +
186A VAL* 1.3 64.0 + - - +
187A ASP* 3.5 2.5 + - - +
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Residues in contact with VAL 186 (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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100A LEU* 3.7 21.8 - - + -
101A TRP 2.8 20.3 + - - +
102A PHE* 3.5 15.8 - - + -
103A LEU* 2.8 35.2 + - - +
132A VAL* 3.9 19.5 - - + -
134A ALA* 4.1 16.8 - - + -
168A ILE* 6.3 0.2 - - + -
172A VAL* 6.1 1.3 - - + -
184A ILE* 4.1 9.9 - - + -
185A LEU* 1.3 73.2 - - - +
187A ASP* 1.3 56.4 + - - +
188A THR* 3.5 19.2 + - + +
205A LEU* 4.3 6.3 - - + -
209A LEU* 4.2 11.4 - - + -
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Residues in contact with ASP 187 (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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103A LEU* 4.5 6.9 - - - +
111A LYS* 3.7 5.9 - - - +
112A THR* 2.4 53.8 + - - +
115A ALA* 4.4 10.3 - - + -
132A VAL 2.9 17.2 + - - +
133A ALA* 5.0 2.4 - - - -
134A ALA* 3.0 28.7 + - - +
135A ASP* 3.8 7.3 + - - +
141A ALA* 5.2 2.8 - - - +
145A LEU* 4.0 18.1 - - + +
185A LEU 3.5 2.2 + - - -
186A VAL* 1.3 68.5 - - - +
188A THR* 1.3 71.1 + - - +
1002A MG 4.0 2.0 - - - -
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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