Contacts of the strand formed by residues 309 - 313 (chain A) in PDB entry 1V2E
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 309 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A GLY* 3.9 13.0 - - - -
163A ASN* 3.4 30.7 - - + +
164A PRO* 4.3 10.8 - - + +
166A GLY* 4.8 0.5 - - - -
194A TYR* 3.0 24.7 - + - -
304A PRO* 3.4 22.9 - - - +
307A THR* 3.3 22.3 + - - +
308A TYR* 1.3 91.8 - + - +
310A LEU* 1.3 63.3 + - - +
347A ARG* 3.3 41.3 - - + -
348A PHE 3.3 10.3 - - - +
349A ALA* 4.2 8.5 - - + -
350A PHE* 3.5 1.5 - - - -
520A KMT 3.2 31.0 - - - -
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Residues in contact with LEU 310 (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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164A PRO 4.9 1.3 - - - -
165A THR 5.6 0.9 - - - -
287A ARG* 4.4 5.2 - - + +
290A LEU* 3.9 17.0 - - + -
291A ALA* 3.7 33.7 - - + +
294A LEU* 4.2 9.9 - - + -
301A VAL* 4.0 10.8 - - + -
302A TYR 4.7 0.2 - - - +
304A PRO* 4.1 22.7 - - + -
309A PHE* 1.3 77.0 - - - +
311A MET* 1.3 72.1 + - - +
347A ARG* 3.5 3.7 - - - +
348A PHE* 2.8 60.5 + - + -
350A PHE* 3.7 14.8 - - + -
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Residues in contact with MET 311 (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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110A PRO* 5.3 1.8 - - + -
138A PHE* 3.8 33.7 - - + -
164A PRO* 3.3 46.7 - - + +
165A THR* 4.2 4.1 + - - +
301A VAL* 3.9 1.6 - - - +
302A TYR* 2.9 40.7 + - + +
310A LEU* 1.3 78.4 - - - +
312A ALA* 1.3 62.0 + - - +
333A ALA* 4.6 4.7 - - + -
336A PHE* 4.5 9.2 - - + -
337A TYR* 5.4 2.0 - - + -
345A LEU* 3.5 38.1 - - + -
346A PHE 3.5 14.4 - - - +
347A ARG* 4.3 9.6 - - + -
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Residues in contact with ALA 312 (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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294A LEU* 3.9 19.7 - - + -
299A LEU* 5.4 2.0 - - + -
300A ARG 3.3 13.5 - - - +
301A VAL* 4.4 6.1 - - + -
302A TYR* 4.6 0.9 - - - -
310A LEU* 4.2 1.5 + - + -
311A MET* 1.3 75.0 - - - +
313A GLU* 1.3 65.5 + - - +
314A LEU* 4.1 6.7 + - + -
345A LEU* 3.6 3.7 - - - +
346A PHE* 2.9 33.5 + - - +
348A PHE* 3.6 23.1 - - + -
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Residues in contact with GLU 313 (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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133A LEU* 4.0 16.1 - - - +
299A LEU* 3.2 23.4 - - - +
300A ARG* 3.0 31.7 + - + +
302A TYR* 2.7 31.6 + - + -
312A ALA* 1.3 73.1 - - - +
314A LEU* 1.3 63.0 + - - +
315A PRO* 3.3 6.6 - - + +
342A PRO* 4.9 3.3 - - - +
343A LYS 4.8 7.3 - - - +
344A ASP* 3.0 13.9 - - + +
345A LEU* 3.6 22.1 - - + +
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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