Contacts of the helix formed by residues 358 - 371 (chain B) in PDB entry 3V4P
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 ASN 358 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351B GLU 3.2 25.7 + - - -
352B LEU* 3.8 7.5 - - - +
353B SER* 2.7 42.0 + - - +
356B SER 3.5 0.2 - - - -
357B SER* 1.3 78.8 + - - +
359B VAL* 1.3 57.5 + - - +
360B VAL 3.7 0.7 - - - -
361B GLN* 4.5 5.9 - - + +
362B LEU* 3.2 20.2 + - - +
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Residues in contact with VAL 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B TYR* 4.1 27.6 - - + +
152B VAL* 4.9 3.4 - - + -
155B LEU* 3.9 21.5 - - + -
266B VAL* 5.2 1.1 - - + -
268B THR* 6.1 0.2 - - - -
328B ALA* 5.2 10.1 - - + -
352B LEU* 3.8 19.5 - - + -
356B SER 3.3 19.3 - - - +
357B SER 3.1 1.7 - - - +
358B ASN* 1.3 75.3 - - - +
360B VAL* 1.3 71.0 + - + +
361B GLN 3.2 2.0 - - - -
362B LEU* 3.0 6.8 + - + +
363B ILE* 2.9 44.8 + - + +
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Residues in contact with VAL 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B LEU* 3.6 46.0 - - + +
158B ALA* 4.0 12.1 - - + +
159B LEU* 3.8 29.2 - - + +
162B ARG* 3.8 28.7 - - + +
357B SER 4.4 4.9 + - - +
359B VAL* 1.3 79.5 - - + +
361B GLN* 1.3 59.1 + - - +
363B ILE* 4.0 3.5 + - - +
364B MET* 3.3 22.7 + - - +
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Residues in contact with GLN 361 (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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162B ARG* 3.9 29.1 - - - +
358B ASN* 4.4 6.8 + - + +
359B VAL 3.2 0.6 - - - +
360B VAL* 1.3 77.2 - - - +
362B LEU* 1.3 67.1 + - - +
363B ILE 3.2 0.4 - - - -
364B MET* 2.9 3.3 + - - +
365B ASP* 2.9 45.1 + - - +
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Residues in contact with LEU 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B ILE* 5.9 3.6 - - + -
328B ALA* 3.7 30.7 - - + -
350B GLY* 3.6 28.9 - - - +
351B GLU 3.3 29.2 - - - +
352B LEU* 4.3 9.9 - - + -
358B ASN* 3.2 19.4 + - - +
359B VAL* 3.0 7.9 + - + +
361B GLN* 1.3 78.7 - - - +
363B ILE* 1.3 56.8 + - + +
365B ASP* 3.5 10.4 + - + +
366B ALA* 2.9 33.5 + - + +
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Residues in contact with ILE 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU* 4.3 21.5 - - + -
137B TYR* 4.8 4.5 - - + -
159B LEU* 4.1 22.9 - - + -
163B LEU* 5.3 0.4 - - + -
264B LEU* 5.3 3.6 - - + -
266B VAL* 3.8 25.8 - - + -
326B ILE* 4.4 20.5 - - + +
359B VAL* 2.9 37.9 + - + +
360B VAL* 4.0 5.2 - - - +
362B LEU* 1.3 76.7 - - + +
364B MET* 1.3 73.9 + - + +
366B ALA* 3.3 8.2 + - - +
367B TYR* 2.9 27.3 + - + +
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Residues in contact with MET 364 (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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159B LEU* 4.7 3.1 - - + -
162B ARG* 3.6 57.7 - - + +
163B LEU* 3.5 29.4 - - + -
166B VAL* 5.1 9.0 - - - -
360B VAL 3.3 17.0 - - - +
361B GLN 2.9 7.0 + - - +
363B ILE* 1.3 91.5 - - + +
365B ASP* 1.3 63.3 + - - +
367B TYR* 3.0 14.1 + - + +
368B ASN* 2.9 40.6 + - - +
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Residues in contact with ASP 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B GLN* 2.9 44.5 + - - +
362B LEU* 3.9 10.5 - - + +
364B MET* 1.3 78.0 - - - +
366B ALA* 1.3 61.9 + - - +
368B ASN* 4.2 8.9 - - - +
369B SER* 3.2 21.7 + - - -
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Residues in contact with ALA 366 (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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326B ILE* 3.7 21.8 - - + -
348B ALA* 3.7 25.6 - - + +
349B VAL 6.2 0.4 - - - -
350B GLY* 6.0 2.7 - - - +
362B LEU* 2.9 22.3 + - + +
363B ILE 3.3 6.3 - - - +
365B ASP* 1.3 78.1 - - - +
367B TYR* 1.3 57.6 + - - +
369B SER* 3.0 8.3 + - - -
370B LEU* 2.9 29.2 + - - +
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Residues in contact with TYR 367 (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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127B ARG* 5.3 1.7 + - - -
131B TYR* 4.3 11.8 + - - +
133B VAL* 3.6 26.1 - - + +
166B VAL* 4.0 30.5 - - + +
167B THR* 6.1 0.2 - - + -
262B SER* 4.3 14.3 + - - -
264B LEU* 3.7 33.9 - - + -
324B GLN* 5.5 2.5 - - - -
326B ILE* 5.3 0.9 - - + -
363B ILE* 2.9 16.6 + - + +
364B MET* 3.0 15.9 + - + +
366B ALA* 1.3 73.4 - - - +
368B ASN* 1.3 67.3 + - - +
369B SER 3.1 2.2 - - - -
370B LEU* 2.8 10.6 + - + -
371B SER* 2.7 65.2 + - - -
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Residues in contact with ASN 368 (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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127B ARG* 4.9 3.8 + - - +
166B VAL* 5.0 13.7 - - - +
364B MET* 2.9 29.9 + - - +
365B ASP* 4.2 9.0 + - - +
367B TYR* 1.3 84.5 - - - +
369B SER* 1.3 57.3 + - - +
371B SER* 4.3 4.0 + - - -
372B SER* 2.9 23.9 + - - -
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Residues in contact with SER 369 (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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348B ALA* 5.0 4.0 - - - +
365B ASP 3.2 12.3 + - - -
366B ALA* 3.0 15.4 + - - -
368B ASN* 1.3 76.4 - - - +
370B LEU* 1.3 60.1 + - - +
372B SER* 3.0 16.5 + - - -
373B THR* 3.1 15.8 + - - -
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Residues in contact with LEU 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B LEU* 3.6 22.9 - - + -
324B GLN* 3.3 29.6 - - + +
326B ILE* 4.2 20.0 - - + -
346B LYS* 3.3 50.7 - - - +
347B SER* 3.7 7.2 - - - +
348B ALA* 4.1 10.3 - - + +
366B ALA 2.9 16.9 + - - +
367B TYR* 2.8 12.3 + - + +
369B SER* 1.3 76.1 - - - +
371B SER* 1.3 60.3 + - - +
372B SER 3.1 4.0 - - - -
373B THR* 3.2 20.4 + - - +
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Residues in contact with SER 371 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ARG* 2.6 45.3 + - - -
262B SER* 6.1 0.2 - - - -
324B GLN* 5.3 1.1 - - - +
346B LYS* 4.5 8.7 - - - +
367B TYR* 2.7 56.3 + - - -
368B ASN* 4.3 2.6 + - - -
370B LEU* 1.3 69.8 - - - +
372B SER* 1.3 54.7 + - - +
373B THR 2.9 14.1 + - - +
374B VAL* 5.0 1.2 - - - +
443B PHE* 4.4 13.6 - - - -
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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