Contacts of the strand formed by residues 340 - 344 (chain B) in PDB entry 4BVH
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 ARG 340 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B VAL* 6.0 0.2 - - - -
315B LEU* 3.4 16.4 - - + +
317B ILE* 4.6 4.9 - - + -
331B THR* 3.0 31.6 + - - -
332B GLU* 2.9 24.9 + - - -
334B VAL* 4.0 15.7 - - + -
338B VAL 3.8 8.3 - - - +
339B PRO* 1.3 79.4 - - - +
341B LEU* 1.3 60.0 + - - +
342B LEU 4.0 0.4 + - - -
350B PRO* 4.0 8.7 + - - +
351B LEU* 3.9 21.6 - - + +
354B HIS 3.7 14.3 + - - -
356B ARG* 3.6 32.2 - - - +
358B ARG 3.4 5.2 + - - +
359B ASP* 2.8 41.7 + - - +
360B VAL* 2.8 28.2 + - - +
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Residues in contact with LEU 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LEU* 3.7 28.7 - - + -
128B VAL* 4.0 25.6 - - + -
314B LEU* 5.0 1.1 - - + +
315B LEU 2.9 7.7 + - - -
316B LEU* 3.4 21.0 - - + +
317B ILE* 2.8 34.7 + - - +
339B PRO 4.2 0.4 - - - -
340B ARG* 1.3 71.9 - - - +
342B LEU* 1.3 63.9 + - - +
343B ILE* 4.0 15.6 + - + +
360B VAL* 3.4 34.8 - - + +
362B GLN* 4.3 3.4 - - + -
373B LEU* 3.9 22.0 - - + -
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Residues in contact with LEU 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B ILE* 3.3 36.6 - - + +
318B LEU* 5.0 0.4 - - - +
319B GLY 5.3 0.2 - - - +
320B THR 4.8 1.1 - - - +
322B LEU* 5.4 0.9 - - + -
340B ARG 4.0 1.0 + - - -
341B LEU* 1.3 74.6 - - - +
343B ILE* 1.3 57.8 + - - +
344B ASN* 3.6 22.0 - - + +
346B ASP 3.6 21.5 - - - +
347B LEU* 3.9 26.5 - - + -
348B VAL* 3.9 19.7 - - + +
351B LEU* 3.7 21.7 - - + +
360B VAL 2.9 11.2 + - - +
361B ALA* 4.4 2.2 - - + -
362B GLN* 2.7 33.1 + - - +
363B LEU* 4.2 6.1 - - + -
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Residues in contact with ILE 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B LEU* 5.1 2.0 - - + -
212B PHE* 5.8 0.7 - - + -
316B LEU* 6.2 0.2 - - + -
317B ILE 2.8 9.5 + - - -
318B LEU* 3.4 28.3 - - + -
319B GLY 3.1 23.0 + - - -
341B LEU* 4.0 19.1 - - + -
342B LEU* 1.3 76.2 - - - +
344B ASN* 1.3 60.4 + - - +
362B GLN* 3.5 13.5 - - + +
365B ASP 4.7 1.1 - - - +
366B VAL* 4.0 26.2 - - + +
369B GLY* 3.8 32.8 - - - +
370B VAL* 4.2 12.8 - - + -
373B LEU* 4.1 26.7 - - + -
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Residues in contact with ASN 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319B GLY* 3.3 8.7 - - - -
320B THR 3.3 34.8 + - - -
342B LEU* 3.6 18.6 - - + +
343B ILE* 1.3 76.4 - - - +
345B ARG* 1.3 65.3 + - - +
346B ASP 2.8 33.7 + - - +
348B VAL* 3.9 6.9 - - - +
362B GLN 3.3 5.3 + - - -
363B LEU* 3.2 10.9 - - - +
364B GLY 3.0 21.4 + - - -
1393B AR6 3.2 36.8 + - - -
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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
------------------------------------------------------------
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