Contacts of the strand formed by residues 182 - 185 (chain D) in PDB entry 6DBV
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 182 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154D VAL* 4.5 7.0 - - + -
155D LEU 3.6 5.6 - - - +
156D PHE* 4.2 17.3 - - + -
181D GLN* 1.3 73.3 - - - +
183D TYR* 1.3 64.6 + - - +
184D LEU* 5.3 2.5 - - + -
194D ALA* 3.7 0.2 - - - -
195D HIS* 2.9 55.4 + - + +
196D THR 4.4 0.7 - - - +
200D LEU* 3.9 23.6 - - + +
218D PHE* 4.9 1.6 - - + -
236D LEU* 4.3 24.5 - - + -
247D LEU* 4.0 24.9 - - + -
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Residues in contact with TYR 183 (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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132D ASP* 4.6 2.9 - - - -
133D VAL 4.6 4.0 - - - -
134D PRO* 3.9 28.0 - - + -
135D SER* 4.8 2.6 + - - -
137D ARG* 3.8 29.3 + - - -
153D CYS 3.7 0.3 - - - +
154D VAL* 3.2 9.4 - - - +
155D LEU* 2.9 59.8 + - + +
178D CYS* 5.1 2.4 - - - -
181D GLN* 3.1 53.9 + - + +
182D VAL* 1.3 73.9 - - - +
184D LEU* 1.3 63.6 + - - +
185D ILE* 4.7 8.0 - - + +
192D CYS* 5.6 0.7 - - + -
193D THR 3.1 17.3 - - - +
194D ALA* 3.5 20.4 - - + +
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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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153D CYS 3.5 6.1 - - - +
154D VAL* 4.4 15.0 - - + -
182D VAL* 5.3 1.8 - - + -
183D TYR* 1.3 81.5 - - - +
185D ILE* 1.3 60.8 + - - +
186D ASP 4.3 0.4 - - - -
191D CYS 4.2 1.3 - - - +
192D CYS* 3.3 6.6 - - - +
193D THR* 2.9 42.3 + - - +
195D HIS* 3.5 25.1 - - + +
238D VAL* 4.9 9.6 - - + -
240D LEU* 5.4 4.5 - - + -
245D PRO* 3.3 43.1 - - + +
247D LEU* 4.8 17.5 - - + -
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Residues in contact with ILE 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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91D LEU* 5.8 0.2 - - + -
93D HIS* 6.0 1.8 - - + +
106D LEU* 4.5 23.3 - - + -
129D LEU* 5.0 6.1 - - + -
134D PRO* 4.8 9.6 - - + -
142D LEU* 4.3 11.2 - - + -
152D ALA* 3.7 4.4 - - - +
153D CYS* 2.9 48.8 + - + +
155D LEU* 4.2 29.4 - - + -
183D TYR* 4.7 4.3 - - + +
184D LEU* 1.3 81.5 - - - +
186D ASP* 1.3 71.9 + - - +
187D LEU* 4.6 7.5 - - + +
192D CYS* 3.6 28.5 - - + +
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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