Contacts of the strand formed by residues 348 - 352 (chain A) in PDB entry 1VPE
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 ILE 348 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A PHE* 3.9 23.1 - - + -
180A LYS* 5.8 7.2 - - + +
181A VAL* 3.7 30.3 - - + -
312A LYS 2.9 13.0 + - - +
313A THR* 3.3 10.2 - - + +
314A VAL 2.9 25.3 + - - +
346A GLY 3.8 4.9 + - - +
347A ALA* 1.3 71.8 - - - +
349A THR* 1.3 61.2 + - - +
350A VAL* 4.4 3.8 - - + -
370A SER* 3.5 13.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A VAL* 3.5 9.2 - - + -
339A ILE* 3.6 33.2 - - + +
342A LEU* 4.4 2.5 - - + -
343A THR* 2.7 33.7 + - - +
347A ALA* 4.0 15.0 - - + +
348A ILE* 1.3 77.9 - - - +
350A VAL* 1.3 62.6 + - - +
369A PHE* 3.3 9.7 - - - +
370A SER* 3.0 34.9 + - - -
371A HIS 3.1 9.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A PHE* 3.8 26.5 - - + -
178A LEU* 4.1 21.8 - - + -
181A VAL* 4.4 14.1 - - + -
313A THR* 6.0 0.2 - - + -
314A VAL* 2.9 16.1 + - - +
315A VAL* 4.3 17.5 - - + -
316A TRP* 2.8 34.1 + - - +
339A ILE* 5.7 1.3 - - - +
348A ILE* 4.4 3.1 - - + -
349A THR* 1.3 77.7 - - - +
351A VAL* 1.3 69.9 + - - +
352A GLY* 4.1 3.1 + - - +
371A HIS* 3.3 17.0 - - + +
373A SER* 5.6 1.6 - - - -
379A SER* 5.8 4.0 - - - +
383A LEU* 6.4 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A TRP* 3.4 23.3 - - + +
339A ILE* 5.7 0.2 - - + -
350A VAL* 1.3 78.6 - - - +
352A GLY* 1.3 56.1 + - - +
356A SER* 3.7 37.7 - - - +
357A ALA* 4.3 5.6 - - - +
360A VAL* 4.2 6.3 - - + -
369A PHE* 3.5 46.4 - - + -
371A HIS 2.9 8.9 + - - +
372A VAL* 3.4 9.2 - - + -
373A SER* 2.6 34.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A VAL* 6.2 0.8 - - - +
316A TRP 2.9 9.3 + - - +
317A ASN* 3.2 29.5 - - - +
350A VAL* 4.1 4.5 - - - +
351A VAL* 1.3 75.0 - - - +
353A GLY* 1.3 60.3 + - - -
356A SER* 3.6 5.2 + - - -
373A SER* 3.1 11.2 - - - -
376A GLY* 3.9 6.5 - - - -
379A SER* 4.3 15.5 - - - -
----------------------------------------------------------
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