Contacts of the strand formed by residues 183 - 187 (chain D) in PDB entry 3COG
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 ILE 183 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100D LEU* 4.1 15.5 - - + -
101D LEU* 4.7 8.3 - - + -
152D LYS* 2.9 19.2 + - + +
153D LEU* 3.4 16.7 - - + +
154D VAL 2.8 28.4 + - - +
176D VAL* 4.5 0.2 - - - -
181D ASP* 5.5 3.8 - - - +
182D ILE* 1.3 77.2 - - - +
184D LEU* 1.3 65.6 + - - +
185D VAL* 4.1 0.2 - - + -
204D ASP* 3.4 15.9 - - + +
205D ILE* 4.0 26.0 - - + -
232D LEU* 3.9 29.2 - - + -
235D ARG* 4.4 17.9 - - - +
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Residues in contact with LEU 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D VAL* 3.6 30.7 - - + +
156D ILE* 4.2 12.8 - - + -
169D ILE* 4.1 9.6 - - + +
172D CYS* 4.2 8.1 - - + +
173D ALA* 3.6 40.6 - - + +
176D VAL* 4.2 15.7 - - + -
177D HIS* 4.4 2.5 - - - +
182D ILE 3.8 0.6 + - - -
183D ILE* 1.3 70.5 - - - +
185D VAL* 1.3 69.8 + - - +
186D VAL* 4.7 1.3 - - + -
202D GLY 4.5 0.2 - - - +
203D ALA* 3.8 19.7 - - + +
204D ASP* 2.7 44.5 + - - +
205D ILE 3.2 6.8 + - - -
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Residues in contact with VAL 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D ILE* 4.0 5.4 - - + -
153D LEU* 3.7 24.9 - - + -
154D VAL 2.9 12.7 + - - +
155D TRP* 3.7 38.4 - - + -
156D ILE* 2.9 32.7 + - - +
183D ILE* 3.9 1.1 + - + -
184D LEU* 1.3 75.5 - - - +
186D VAL* 1.3 77.9 + - - +
187D ASP 4.2 1.1 - - - +
205D ILE* 3.6 33.9 - - + -
207D MET* 4.1 11.7 - - + -
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Residues in contact with VAL 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D ILE* 3.4 23.3 - - + +
158D THR* 4.1 22.9 - - + -
169D ILE* 4.0 13.9 - - + -
184D LEU* 4.7 3.8 - - + -
185D VAL* 1.3 76.6 - - - +
187D ASP* 1.3 71.1 + - - +
188D ASN* 3.3 5.6 + - + +
196D GLN* 4.6 1.3 - - - +
198D PRO* 3.6 30.1 - - + -
203D ALA* 3.6 23.3 - - + -
205D ILE 2.9 7.9 + - - -
206D SER* 3.5 3.6 - - - -
207D MET 2.8 25.8 + - - -
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Residues in contact with ASP 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D THR* 4.8 1.0 + - - -
155D TRP* 4.2 14.7 + - + +
156D ILE 2.8 16.5 + - - +
157D GLU* 3.7 33.2 - - + +
158D THR 3.9 8.3 + - - +
159D PRO 5.5 0.3 - - - +
185D VAL* 4.1 1.6 - - - +
186D VAL* 1.3 71.3 - - - +
188D ASN* 1.3 57.5 + - - +
189D THR* 2.6 30.5 + - - -
190D PHE 5.1 0.9 + - - -
207D MET* 3.4 27.1 - - - +
500D PLP 2.7 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