Contacts of the strand formed by residues 360 - 369 (chain A) in PDB entry 2V4L
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 360 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358A ASP 4.0 0.4 + - - -
359A ARG* 1.3 91.5 - - - +
361A PHE* 1.3 64.3 + - - +
362A ARG* 3.6 6.2 + - - +
415A GLU* 3.4 41.1 + - + +
416A PHE 3.1 26.5 - - - +
417A SER* 4.5 13.0 - - - +
418A ILE 3.3 9.9 - - - +
419A LYS* 4.0 7.9 - - + +
420A ILE* 4.2 3.3 - - - +
522A ASN* 5.0 0.7 - - - +
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Residues in contact with PHE 361 (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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359A ARG 3.7 2.6 + - - -
360A LYS* 1.3 72.1 - - - +
362A ARG* 1.3 67.4 + - - +
363A VAL* 4.2 4.5 - - + -
387A ILE* 3.5 21.1 - - + -
415A GLU* 4.1 0.5 - - - -
416A PHE* 3.1 60.7 + + + +
418A ILE* 3.0 16.0 + - + +
419A LYS 4.9 0.2 - - - -
420A ILE* 3.4 30.4 - - + +
423A LEU* 4.1 17.3 - - + -
429A LEU* 4.6 5.8 - - + -
468A LEU* 3.3 31.2 - - + -
475A LEU* 5.0 2.2 - - + -
520A LEU* 3.7 24.5 - - + -
522A ASN* 3.6 18.6 - - - -
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Residues in contact with ARG 362 (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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359A ARG* 6.0 8.6 - - - +
360A LYS 4.3 6.3 - - - +
361A PHE* 1.3 85.1 - - - +
363A VAL* 1.3 59.9 + - - +
413A TRP* 3.4 68.3 - - + +
414A LEU 3.3 16.2 - - - +
415A GLU* 4.0 16.4 - - - +
519A LEU 4.5 0.9 - - - +
520A LEU* 4.0 12.8 - - - +
521A ASP* 4.3 16.9 + - - +
522A ASN* 3.9 16.5 + - - +
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Residues in contact with VAL 363 (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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361A PHE* 4.2 5.8 - - + -
362A ARG* 1.3 75.3 - - - +
364A LYS* 1.3 71.8 + - - +
365A ILE* 3.7 13.8 + - + -
385A ALA* 4.5 7.4 - - + -
413A TRP* 3.7 5.1 - - - -
414A LEU* 2.9 35.0 + - + +
416A PHE* 3.7 24.7 - - + -
429A LEU* 4.1 14.4 - - + -
518A ILE* 3.9 19.1 - - + -
519A LEU 3.9 2.9 - - - +
520A LEU* 3.6 23.6 - - + -
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Residues in contact with LYS 364 (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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363A VAL* 1.3 71.4 - - - +
365A ILE* 1.3 64.8 + - - +
366A ARG* 3.5 36.2 + - + +
411A ASN* 3.5 29.6 + - - +
412A VAL 3.4 17.9 - - - +
413A TRP* 3.7 42.9 - - + +
518A ILE* 3.0 29.8 - - - +
519A LEU* 3.0 33.1 + - + +
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Residues in contact with ILE 365 (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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363A VAL* 4.5 14.1 - - + +
364A LYS* 1.3 72.4 - - - +
366A ARG* 1.3 61.3 + - - +
367A GLY* 4.3 4.9 - - - +
383A VAL* 3.9 19.7 - - + -
385A ALA* 5.0 0.4 - - + -
399A THR* 4.1 15.3 - - + -
410A TRP* 3.5 27.7 - - + +
411A ASN 3.2 18.0 + - - -
412A VAL* 3.1 14.5 + - + +
414A LEU* 3.8 28.3 - - + -
431A LEU* 4.5 9.2 - - + -
516A ILE* 4.2 19.5 - - + -
517A SER 3.9 1.8 - - - -
518A ILE* 4.1 17.9 - - + -
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Residues in contact with ARG 366 (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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364A LYS* 3.9 27.2 - - + +
365A ILE* 1.3 72.0 - - - +
367A GLY* 1.3 55.9 - - - +
409A LEU* 3.5 16.1 - - + +
410A TRP 3.2 19.9 + - - -
411A ASN* 3.7 14.3 + - - +
479A GLU* 2.6 47.5 + - - -
517A SER* 2.8 36.8 + - - +
518A ILE* 4.4 4.7 - - - +
519A LEU* 3.4 32.1 - - - +
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Residues in contact with GLY 367 (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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365A ILE* 3.4 3.2 - - - +
366A ARG* 1.3 83.5 - - - +
368A ILE* 1.3 65.1 + - - +
369A ASP* 4.2 2.1 - - - +
408A VAL 3.2 12.8 - - - -
409A LEU* 4.1 6.7 - - - -
410A TRP* 4.4 9.9 - - - -
516A ILE* 3.5 5.5 - - - +
517A SER* 3.0 29.0 + - - -
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Residues in contact with ILE 368 (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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367A GLY* 1.3 79.0 - - - +
369A ASP* 1.3 67.3 + - - +
381A VAL* 3.9 28.5 - - + -
383A VAL* 4.1 8.7 - - + -
404A PHE* 4.5 5.2 - - + -
405A THR 5.4 0.7 - - - +
406A GLU 4.8 0.4 - - - +
407A GLU* 3.7 3.6 - - - +
408A VAL* 2.9 57.7 + - + +
409A LEU* 5.5 0.7 - - - +
410A TRP* 4.2 5.4 - - + -
433A ILE* 3.7 26.0 - - + -
514A MET* 3.8 23.1 - - + -
515A SER 3.3 10.3 - - - +
516A ILE* 3.7 16.6 - - + -
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Residues in contact with ASP 369 (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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367A GLY 4.2 4.7 - - - +
368A ILE* 1.3 82.4 - - - +
370A ILE* 1.3 61.1 + - - +
371A PRO* 5.0 0.2 - - - +
406A GLU 3.6 9.4 - - - +
407A GLU* 4.7 11.4 - - + -
481A VAL* 5.8 0.4 - - - +
513A SER 4.2 1.4 - - - +
514A MET* 3.7 3.5 - - - -
515A SER* 2.9 51.3 + - - +
517A SER* 4.4 9.7 + - - -
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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