Contacts of the strand formed by residues 150 - 154 (chain D) in PDB entry 2VKM
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 PHE 150 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D THR* 3.9 16.4 - - + -
121D LEU* 3.9 34.5 - - + -
137D PHE* 3.8 30.5 - + + -
149D LEU* 1.3 78.8 - - - +
151D SER* 1.3 64.1 + - - +
152D LEU* 4.3 13.5 - - + -
174D MET* 5.0 4.9 - - + -
175D ILE 3.3 13.9 - - - +
176D ILE* 4.3 7.6 - - + -
177D GLY 4.3 0.2 - - - +
178D GLY 4.5 2.0 - - - -
199D TYR* 3.3 24.9 - - - -
344D VAL* 3.8 1.4 - - - +
345D PHE* 2.8 64.9 + + + +
347D ARG* 3.9 9.9 - - - -
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Residues in contact with SER 151 (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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150D PHE* 1.3 77.2 - - - +
152D LEU* 1.3 65.6 + - - +
173D SER 3.8 0.3 - - - +
174D MET* 3.3 5.9 - - - +
175D ILE* 2.9 36.2 + - - +
178D GLY 2.8 17.5 + - - -
179D ILE* 4.8 0.2 - - - -
342D TYR* 2.7 35.6 + - - -
343D VAL 3.3 10.8 - - - -
344D VAL* 4.1 13.9 - - - -
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Residues in contact with LEU 152 (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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6D LEU* 4.4 7.4 - - + -
31D VAL* 3.8 23.6 - - + -
33D THR* 3.9 24.2 - - + -
150D PHE* 4.3 6.5 - - + -
151D SER* 1.3 77.7 - - - +
153D GLN* 1.3 59.3 + - - +
154D LEU* 4.0 9.6 - - + -
173D SER 3.5 2.9 - - - +
174D MET* 3.6 35.9 - - + -
229D SER* 4.1 6.5 - - - -
338D MET* 3.7 31.3 - - + +
341D PHE 3.9 2.3 - - - +
342D TYR* 3.5 5.8 - - - -
343D VAL* 2.8 38.0 + - - +
345D PHE* 3.9 6.7 - - + -
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Residues in contact with GLN 153 (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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4D ASP* 4.8 4.5 - - - +
152D LEU* 1.3 73.4 - - - +
154D LEU* 1.3 63.8 + - - +
155D CYS* 3.3 14.0 - - - -
172D GLY* 3.1 8.7 - - - -
173D SER* 2.9 41.8 + - - +
183D LEU* 3.0 54.1 + - + +
341D PHE 4.5 3.6 - - - -
342D TYR* 3.9 15.2 - - + -
357D SER* 3.6 14.3 + - - +
358D ALA* 4.1 3.4 - - - +
359D CYS* 3.6 31.5 - - - +
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Residues in contact with LEU 154 (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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6D LEU* 3.9 18.8 - - + -
14D TYR* 3.7 49.4 - - + -
31D VAL* 5.8 2.2 - - + -
152D LEU* 4.0 13.8 + - + -
153D GLN* 1.3 73.9 - - - +
155D CYS* 1.3 62.6 + - - +
156D GLY 4.0 0.2 - - - -
171D GLY 3.9 1.8 - - - -
229D SER* 4.1 25.6 - - - +
335D ALA* 5.0 6.7 - - + -
338D MET* 3.9 41.4 + - + +
339D GLU* 3.4 29.8 - - + +
341D PHE 4.7 0.7 + - - +
357D SER* 5.0 0.5 + - - -
359D CYS* 3.8 4.5 - - - -
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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