Contacts of the strand formed by residues 151 - 154 (chain L) in PDB entry 3VD1
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 151 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131L PHE* 3.8 22.4 - - + -
142L TRP* 3.9 22.4 - - + -
143L THR 3.7 10.8 - - - +
144L TYR* 4.2 7.2 - - + -
150L LYS* 1.3 74.1 - - - +
152L TYR* 1.3 72.6 + - - +
153L CYS* 3.7 22.6 + - + +
159L CYS* 3.9 16.4 - - - -
256L PHE* 4.0 14.1 - - + -
273L ILE* 4.7 3.8 - - + -
290L PHE* 3.8 22.0 - - + -
291L GLU 2.7 11.9 + - - +
292L GLY* 3.4 2.7 - - - -
293L ARG* 2.9 26.4 + - - +
294L ILE* 5.9 1.3 - - + -
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Residues in contact with TYR 152 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142L TRP* 3.0 16.0 - - - -
143L THR 2.9 23.0 + - - +
145L SER* 4.6 5.0 - - - -
148L LEU* 5.8 0.5 - - - +
150L LYS* 3.3 37.8 - - + +
151L LEU* 1.3 75.6 - - - +
153L CYS* 1.3 58.4 + - - +
293L ARG* 3.5 31.9 - - + +
295L CYS* 4.5 1.8 - - - -
298L PRO* 2.8 33.1 - - + +
301L ASP* 3.6 8.3 - - + -
302L ARG* 3.5 47.3 - - + +
305L ASP* 2.4 41.7 + - - +
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Residues in contact with CYS 153 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141L THR* 3.6 4.3 - - - -
142L TRP* 3.9 11.0 - - + -
151L LEU* 3.7 19.3 + - + -
152L TYR* 1.3 76.2 - - - +
154L GLN* 1.3 75.9 + - - +
157L LYS* 4.2 9.2 - - - -
158L THR 5.1 0.4 - - - -
159L CYS* 3.2 38.8 - - - -
256L PHE* 4.1 14.8 - - + -
293L ARG 3.4 4.8 + - - -
294L ILE* 3.1 11.4 - - + -
295L CYS* 2.9 24.1 + - - +
298L PRO* 4.1 2.7 - - - -
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Residues in contact with GLN 154 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139L SER* 3.7 11.2 + - - +
140L ALA 2.7 27.6 - - - +
141L THR* 2.9 17.7 + - - +
153L CYS* 1.3 89.2 - - - +
155L ILE* 1.3 74.9 + - + +
156L ALA 3.5 1.7 + - - -
157L LYS* 3.0 50.2 + - + +
256L PHE* 4.2 3.8 - - - +
294L ILE* 4.0 3.5 - - - +
295L CYS 3.5 13.9 - - - +
296L ALA* 3.2 22.3 + - - +
298L PRO* 3.2 2.7 - - + +
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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