Contacts of the strand formed by residues 173 - 176 (chain A) in PDB entry 2FV7
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 LYS 173 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A LYS 3.3 21.6 + - - +
148A VAL* 3.3 7.4 - - + +
149A MET* 2.8 29.1 + - - +
171A GLY 3.8 2.8 + - - -
172A VAL* 1.3 71.0 - - - +
174A THR* 1.3 65.8 + - - +
194A ASP* 3.5 23.0 - - + +
195A VAL* 4.9 1.8 - - + -
279A LEU* 4.2 40.4 - - + +
506A UNX 2.5 33.3 - - - -
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Residues in contact with THR 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A MET* 3.5 4.7 - - + -
164A LEU* 3.7 31.9 - - + +
167A ALA* 3.5 32.3 - - + -
168A ARG* 4.0 5.1 + - + +
172A VAL 3.5 6.3 - - - +
173A LYS* 1.3 74.1 - - - +
175A LEU* 1.3 59.6 + - - +
176A PHE 4.0 0.7 - - - -
192A LEU 2.8 25.0 + - - +
193A SER* 3.6 0.4 - - - -
194A ASP* 3.0 25.9 + - - +
195A VAL* 2.9 27.0 + - - +
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Residues in contact with LEU 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A VAL* 4.0 10.1 - - + -
149A MET 2.9 13.2 + - - +
150A VAL* 3.3 13.9 - - + +
151A CYS* 3.2 25.1 + - - +
164A LEU* 5.1 1.3 - - - +
173A LYS 3.9 0.4 + - - -
174A THR* 1.3 72.9 - - - +
176A PHE* 1.3 59.5 + - - +
195A VAL* 3.4 34.3 - - + +
197A CYS* 4.3 13.0 - - + -
272A VAL* 3.8 20.2 - - + +
275A LEU* 4.2 11.0 - - + -
276A ALA* 3.7 39.9 - - + +
279A LEU* 4.0 13.5 - - + -
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Residues in contact with PHE 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A CYS* 3.6 17.5 - - + -
152A GLN 3.7 23.3 - - - -
153A LEU* 3.8 14.1 - - + -
160A SER* 5.0 1.1 - - - -
164A LEU* 4.3 17.0 - - + -
174A THR 4.0 0.6 - - - -
175A LEU* 1.3 76.2 - - - +
177A ASN* 1.3 67.4 + - - +
178A PRO* 3.5 32.6 - - + +
185A LEU* 4.1 2.5 - - + -
189A PHE* 3.4 38.8 - + + -
193A SER* 3.2 29.8 - - - +
195A VAL 2.8 9.5 + - - -
196A PHE* 3.5 24.1 - + + -
197A CYS* 2.9 27.0 + - - +
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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