Contacts of the strand formed by residues 304 - 309 (chain A) in PDB entry 3VF3
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 ASP 304 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256A CYS* 4.2 18.8 - - + +
257A TRP 3.2 15.5 - - - +
258A GLN* 3.8 16.1 - - - +
259A ALA* 4.3 3.8 - - - +
301A THR* 3.1 19.2 + - - +
302A SER* 3.0 10.2 - - - +
303A GLN* 1.3 96.4 - - - +
305A ASP* 1.3 67.9 + - - +
306A CYS* 3.9 3.4 + - - -
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Residues in contact with ASP 305 (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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256A CYS* 3.2 1.4 - - - -
257A TRP 2.9 37.1 + - - +
258A GLN 5.1 0.2 - - - +
259A ALA* 3.6 6.5 - - - +
260A GLY* 3.0 31.3 + - - +
262A THR* 4.1 5.5 + - - +
302A SER 5.6 0.2 - - - +
304A ASP* 1.3 76.9 - - - +
306A CYS* 1.3 60.3 + - - +
307A TYR* 3.5 32.1 + - + +
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Residues in contact with CYS 306 (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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254A LEU* 4.3 16.8 - - + -
255A VAL 3.2 4.3 - - - +
256A CYS* 2.0 46.0 - - - -
295A PRO* 3.5 4.3 - - - +
296A VAL 3.0 29.9 + - - +
301A THR* 3.9 37.7 - - - +
304A ASP* 3.9 3.9 + - - -
305A ASP* 1.3 73.9 - - - +
307A TYR* 1.3 67.9 + - - +
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Residues in contact with TYR 307 (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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248A PHE* 4.2 0.2 - - - -
253A GLN 3.9 0.3 - - - +
254A LEU* 3.4 8.2 - - - -
255A VAL* 2.9 40.0 + - + +
257A TRP* 3.7 22.4 - + + -
262A THR* 2.8 30.5 + - + -
264A TRP* 3.5 28.7 - + - -
293A LEU* 3.6 35.2 - - + -
294A ARG 3.2 7.6 - - - +
295A PRO* 3.7 26.0 - - + -
296A VAL 4.4 0.7 - - - +
305A ASP* 3.5 34.9 + - + +
306A CYS* 1.3 76.4 - - - +
308A LYS* 1.3 64.7 + - - +
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Residues in contact with LYS 308 (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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248A PHE* 4.4 2.5 - - - -
251A GLY 3.8 20.2 - - - +
252A GLU* 3.7 33.2 + - - +
253A GLN 4.2 10.8 - - - +
254A LEU* 3.7 28.9 - - + -
293A LEU* 3.6 4.3 - - - -
294A ARG* 2.9 60.6 + - + +
296A VAL* 3.7 13.5 - - + +
307A TYR* 1.3 75.2 - - - +
309A PHE* 1.3 63.6 + - - +
310A ALA* 3.3 0.6 + - - -
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Residues in contact with PHE 309 (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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220A ASN* 4.3 3.5 + - - -
228A PHE* 4.4 0.4 - + - -
231A ALA* 6.4 0.2 - - + -
232A VAL* 4.2 17.7 - - + -
235A ILE* 4.1 15.3 - - + -
248A PHE* 3.3 38.1 + + + +
249A TRP* 3.7 56.1 - + - -
251A GLY* 3.4 22.1 - - - +
253A GLN 4.9 0.2 + - - -
292A TYR* 4.0 9.4 - + - -
293A LEU* 4.2 15.5 - - + -
308A LYS* 1.3 69.7 - - - +
310A ALA* 1.3 61.5 + - - +
311A ILE* 3.3 63.6 + - + +
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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