Contacts of the strand formed by residues 180 - 184 (chain C) in PDB entry 2ID5
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 VAL 180 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155C GLU 2.8 9.9 + - - +
156C GLN* 3.4 18.4 - - + -
157C LEU 3.0 25.3 + - - +
178C LEU* 3.7 3.3 - - - +
179C ILE* 1.3 93.4 - - + +
181C LEU* 1.3 62.4 + - - +
182C ARG* 3.9 34.5 - - + +
202C LEU* 4.1 1.6 - - - -
204C VAL* 3.4 34.5 - - + +
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Residues in contact with LEU 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C LEU* 3.6 35.0 - - + +
172C LEU* 4.2 15.9 - - + -
178C LEU* 3.8 6.3 - - + -
180C VAL* 1.3 75.3 - - - +
182C ARG* 1.3 69.4 + - - +
183C LEU* 4.0 22.7 - - + -
196C PHE* 3.8 33.4 - - + -
199C LEU* 4.5 10.5 - - + -
202C LEU* 3.7 16.9 - - + +
204C VAL 2.9 9.9 + - - +
205C LEU* 3.5 14.1 - - + +
206C GLU 3.0 23.7 + - - -
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Residues in contact with ARG 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156C GLN* 3.6 23.9 - - - +
157C LEU 3.0 12.1 + - - +
158C THR* 4.1 20.8 + - + +
159C LEU* 2.9 28.9 + - - +
180C VAL* 3.9 20.9 - - + +
181C LEU* 1.3 78.6 - - - +
183C LEU* 1.3 64.4 + - - +
184C ARG* 3.1 33.1 + - - +
204C VAL* 5.7 3.6 - - - +
206C GLU* 3.1 37.3 + - + +
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Residues in contact with LEU 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C LEU* 3.5 37.7 - - + -
167C ILE* 4.6 9.2 - - + -
168C PRO* 5.5 3.1 - - + -
172C LEU* 5.2 5.2 - - + -
181C LEU* 4.0 22.2 - - + -
182C ARG* 1.3 74.5 - - - +
184C ARG* 1.3 60.7 + - - +
186C LEU* 4.0 8.5 - - + -
196C PHE* 4.4 25.6 - - + -
205C LEU* 4.6 2.0 - - + -
206C GLU 2.8 11.7 + - - +
207C ILE* 3.5 12.2 - - + -
208C SER 2.9 25.5 + - - -
210C TRP* 3.0 41.8 + - + -
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Residues in contact with ARG 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C GLU* 5.5 2.6 + - - -
158C THR* 4.2 15.4 + - + +
159C LEU 3.1 5.9 + - - -
160C GLU* 3.2 27.7 + - + +
161C LYS 3.1 17.7 + - - -
182C ARG* 3.1 38.5 - - + +
183C LEU* 1.3 80.2 - - - +
185C HIS* 1.3 82.4 + - + +
186C LEU* 3.3 6.8 + - - +
206C GLU* 2.9 37.3 + - - +
208C SER* 3.2 12.8 + - - +
209C HIS* 5.7 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