Contacts of the strand formed by residues 375 - 382 (chain A) in PDB entry 2V3E
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 VAL 375 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLN* 2.9 17.2 + - - +
310A VAL* 5.3 1.6 - - + -
324A LEU* 3.8 23.8 - - + -
336A LEU* 3.3 22.0 - - + +
337A PHE* 3.9 0.9 - - - -
338A ALA 3.4 17.0 - - - +
370A ASN* 3.2 45.3 + - + +
371A LEU* 3.5 15.6 - - + +
373A TYR 3.8 4.0 - - - +
374A HIS* 1.3 77.1 - - - +
376A VAL* 1.3 59.1 + - - +
377A GLY 3.2 25.8 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
76A GLN* 3.9 10.3 - - + -
77A LYS 3.3 24.9 - - - +
78A VAL* 3.4 9.8 - - - +
79A LYS* 2.6 37.6 + - + +
80A GLY 3.3 1.9 + - - -
335A MET* 3.7 44.4 - - + -
336A LEU 2.8 20.6 + - - +
337A PHE* 4.0 6.5 - - + -
371A LEU* 5.3 1.8 - - - -
374A HIS 3.7 15.0 - - - +
375A VAL* 1.3 72.1 - - - +
377A GLY* 1.3 58.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 377 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLY 2.9 15.0 - - - -
81A PHE* 4.8 5.6 - - - -
337A PHE* 3.7 18.7 - - - -
338A ALA* 2.9 22.3 + - - +
371A LEU* 5.4 2.2 - - - +
375A VAL* 3.2 10.9 + - - +
376A VAL* 1.3 83.6 - - - +
378A TRP* 1.3 61.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLY 3.0 6.7 + - - -
81A PHE* 3.3 42.9 - - + +
82A GLY 3.4 2.9 + - - +
312A TRP* 3.9 10.3 - + - +
337A PHE* 4.3 1.0 - - - -
338A ALA* 3.3 25.1 - - + +
341A ALA* 3.5 29.8 - - + -
363A TYR* 3.6 45.3 - + + -
366A SER* 2.8 32.2 + - - -
367A ILE* 3.5 29.7 - - + +
370A ASN* 3.8 16.4 + - + -
377A GLY* 1.3 73.9 - - - -
379A THR* 1.3 69.1 + - - +
380A ASP* 4.0 12.1 - - - -
420A LEU* 3.9 17.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLY 3.5 3.8 - - - -
83A GLY* 3.9 21.1 - - - +
118A ILE* 4.2 13.1 - - + +
120A ARG* 4.2 15.3 - - + -
175A LEU* 5.3 0.7 - - + -
337A PHE* 3.1 24.2 - - + -
338A ALA 2.8 20.0 + - - -
339A SER* 3.5 15.5 - - - +
340A GLU* 3.4 21.3 + - - -
341A ALA* 3.4 4.2 + - - +
378A TRP* 1.3 80.9 + - - +
380A ASP* 1.3 75.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 380 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLY 2.8 16.5 + - - +
83A GLY* 3.2 16.0 - - - -
84A ALA* 3.4 4.5 + - - +
108A TYR* 4.7 2.1 + - - -
116A TYR* 4.4 3.8 + - - +
120A ARG* 5.3 0.3 - - - +
339A SER 4.6 2.3 - - - +
340A GLU* 5.0 0.4 - - - -
341A ALA 3.1 6.4 - - - +
342A CYS* 4.7 0.3 - - - +
363A TYR* 2.4 37.2 + - - -
378A TRP* 4.0 8.3 - - + -
379A THR* 1.3 81.9 - - - +
381A TRP* 1.3 76.8 + - - +
382A ASN 3.6 9.2 - - - +
383A LEU* 5.0 1.2 - - - +
401A PRO* 3.0 28.5 - - - +
420A LEU* 3.9 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 381 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLY* 3.8 1.0 - - - -
84A ALA* 2.8 41.1 + - + -
86A THR* 3.4 26.7 - - + -
120A ARG* 3.7 25.6 - - - -
122A PRO* 4.4 2.9 - - + -
126A CYS* 3.8 7.9 - - - -
127A ASP* 3.9 8.5 - - - -
128A PHE* 3.4 8.0 - + - -
179A TRP* 3.2 26.5 - + - -
340A GLU* 3.7 21.3 - - + -
341A ALA 3.0 18.9 + - - +
342A CYS* 3.8 27.6 - - + -
380A ASP* 1.3 83.2 + - - +
382A ASN* 1.3 94.6 + - - +
383A LEU 3.2 0.2 + - - -
1502A NND 3.0 36.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 382 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ALA* 3.7 7.9 - - - -
86A THR* 2.6 30.5 + - - +
128A PHE* 3.2 34.4 - - - +
380A ASP* 3.6 8.7 - - - +
381A TRP* 1.3 106.6 - - - +
383A LEU* 1.3 60.5 + - - +
384A ALA 3.9 3.1 - - - +
385A LEU* 3.7 36.0 - - + +
398A VAL* 3.9 1.4 - - - +
399A ASP 5.5 0.9 + - - +
400A SER* 3.0 20.4 + - - -
401A PRO* 4.1 0.3 - - - +
----------------------------------------------------------
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