Contacts of the strand formed by residues 371 - 380 (chain A) in PDB entry 2V40
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 GLU 371 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A TRP* 4.0 5.9 - - + -
369A PHE* 3.7 15.4 - - - +
370A THR* 1.3 85.1 + - - +
372A ILE* 1.3 68.0 + - - +
373A LYS* 3.8 24.2 + - + -
404A THR* 3.9 20.6 - - + +
405A LEU 3.4 12.8 - - - +
406A PRO* 5.0 1.1 - - + -
407A GLY 4.0 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A TRP* 3.9 12.6 - - + -
366A LEU* 4.1 17.9 - - + +
369A PHE* 3.8 17.5 - - + -
371A GLU* 1.3 81.4 - - - +
373A LYS* 1.3 74.9 + - - +
374A VAL* 4.1 0.3 + - - +
403A LYS 3.7 0.3 - - - +
404A THR* 3.6 0.9 - - - -
405A LEU* 2.8 36.7 + - + +
406A PRO 4.5 3.1 - - - +
407A GLY* 4.1 15.3 - - - -
408A TRP* 3.4 39.0 - - + -
428A TYR* 3.5 36.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ILE* 5.8 4.6 - - + +
340A TRP* 3.4 62.1 - - + +
341A LEU 4.3 2.1 + - - -
371A GLU* 3.8 20.0 + - - +
372A ILE* 1.3 79.8 - - - +
374A VAL* 1.3 65.3 + - - +
402A TYR* 3.8 24.8 - - + -
403A LYS 3.3 5.2 - - - +
404A THR* 3.8 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A LEU* 3.6 18.4 - - + +
343A LEU* 3.4 40.4 - - + -
372A ILE* 4.5 0.2 - - + -
373A LYS* 1.3 80.9 - - - +
375A GLY* 1.3 66.3 + - - +
376A VAL* 3.4 2.8 + - + +
402A TYR* 3.4 4.1 - - - -
403A LYS* 2.9 33.8 + - + +
405A LEU* 4.2 14.6 - - + -
428A TYR* 3.6 35.9 - - + +
431A PHE* 4.2 12.8 - - + -
432A ILE* 6.0 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A THR* 4.5 3.8 - - - -
341A LEU 2.9 16.4 + - - -
342A ASP* 4.5 2.5 - - - -
343A LEU* 2.8 34.2 + - - +
344A VAL* 3.7 5.6 + - - -
374A VAL* 1.3 69.0 - - - +
376A VAL* 1.3 58.3 + - - +
377A ALA 3.9 0.7 - - - -
400A VAL* 3.6 26.0 - - - -
401A GLN 3.6 1.6 - - - -
402A TYR* 3.5 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A LEU* 4.5 7.8 - - + -
344A VAL* 3.4 11.1 - - - +
374A VAL 3.6 9.9 - - - +
375A GLY* 1.3 78.1 - - - +
377A ALA* 1.3 67.2 + - + +
401A GLN* 2.9 20.9 + - + +
402A TYR 4.2 2.5 - - - +
403A LYS* 4.0 17.5 - - + +
431A PHE* 3.7 34.3 - - + -
435A GLU* 4.2 16.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 377 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A VAL* 3.4 5.9 - - - +
376A VAL* 1.3 82.0 - - + +
378A TYR* 1.3 72.5 + - - +
384A ILE* 4.0 18.4 - - + -
400A VAL* 3.6 1.6 - - - +
401A GLN* 2.8 46.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A PRO* 3.4 11.6 - - + +
342A ASP* 2.7 28.2 + - - -
344A VAL* 3.7 31.0 - - + +
345A LEU* 3.2 20.0 - - + +
377A ALA* 1.3 83.4 - - - +
379A LYS* 1.3 62.2 + - - +
384A ILE* 3.4 6.6 - - - +
385A ILE* 3.0 44.9 + - + +
387A HIS 4.2 12.1 - - - -
388A ILE* 3.7 17.9 - - + -
389A PRO* 4.4 2.5 - - + -
395A LEU* 4.0 17.3 - - + -
398A VAL* 4.1 19.5 - - + -
399A GLU 3.8 2.2 - - - -
400A VAL* 3.9 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A TYR* 1.3 71.7 - - - +
380A LEU* 1.3 61.0 + - - +
381A ASP 4.3 0.2 - - - -
382A GLY* 3.9 26.6 + - - +
383A GLU 3.2 5.6 - - - +
384A ILE* 3.6 38.4 - - + +
385A ILE* 4.7 0.4 - - - -
397A LYS 4.5 0.3 - - - +
398A VAL* 3.4 7.3 - - - -
399A GLU* 2.8 53.6 + - + +
401A GLN* 3.7 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 380 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A TYR 4.3 0.2 - - - -
379A LYS* 1.3 73.6 - - - +
381A ASP* 1.3 91.6 + - - +
382A GLY 3.2 0.2 - - - -
383A GLU* 2.7 25.0 + - - +
385A ILE* 3.9 37.4 - - + +
387A HIS* 5.2 4.5 - - + +
389A PRO* 4.4 2.2 - - + -
394A VAL* 3.7 33.0 - - + +
397A LYS* 3.9 32.3 - - + +
398A VAL* 4.2 8.1 - - + +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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