Contacts of the strand formed by residues 336 - 341 (chain A) in PDB entry 1U7V
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 336 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A LEU 4.1 0.2 - - - +
298A THR* 3.1 6.9 - - - +
299A VAL* 2.9 53.0 + - + +
335A GLY* 1.3 75.4 - - - -
337A ARG* 1.3 74.9 + - - +
338A LEU* 4.0 17.6 + - + +
347A ALA* 4.1 4.3 - - + -
348A GLU 3.3 17.0 - - - +
350A LEU* 4.7 0.4 - - - -
355A ILE* 4.0 22.4 - - + -
416A MET* 4.3 7.9 - - + -
418A PHE* 3.8 17.3 - - + -
438A ILE* 4.6 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A SER* 5.2 8.2 + - - +
297A LEU 3.8 5.4 - - - +
298A THR* 3.9 14.9 + - - +
334A ARG* 3.7 28.9 - - - +
336A VAL* 1.3 75.2 - - - +
338A LEU* 1.3 66.4 + - - +
339A TYR* 3.0 39.5 + - + -
346A PHE 3.4 1.4 - - - +
347A ALA* 3.3 4.5 - - - -
348A GLU* 2.7 60.5 + - + +
350A LEU* 3.8 30.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A TRP* 4.1 12.9 - - + -
275A CYS* 5.2 0.2 - - - -
277A ILE* 3.7 24.2 - - + -
295A PRO 3.8 0.9 - - - +
296A SER* 3.6 7.4 - - - -
297A LEU* 3.0 47.2 + - + +
299A VAL* 4.4 7.6 - - + -
336A VAL* 4.0 19.1 - - + +
337A ARG* 1.3 75.4 - - - +
339A TYR* 1.3 63.7 + - - +
345A VAL* 4.9 6.3 - - + -
346A PHE 3.2 10.3 - - - +
347A ALA* 4.2 4.7 - - + -
384A ILE* 6.1 0.9 - - + -
416A MET* 3.6 27.4 - - + -
438A ILE* 6.1 0.4 - - + -
440A LEU* 3.6 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A TRP* 4.5 1.6 - - - -
295A PRO 3.7 5.6 - - - -
296A SER* 5.1 9.6 - - - -
337A ARG* 3.0 51.7 + - + -
338A LEU* 1.3 78.4 - - - +
340A TYR* 1.3 61.3 + - - +
341A ILE* 3.8 28.5 - - + -
344A GLU 4.2 0.2 - - - -
345A VAL* 3.0 32.4 - - - +
346A PHE* 2.9 33.4 + + + +
348A GLU* 3.4 18.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A GLU* 4.9 15.6 + - + -
274A TRP* 3.8 48.7 - + + +
295A PRO* 3.1 31.9 + - + +
339A TYR* 1.3 74.3 - - - +
341A ILE* 1.3 63.0 + - - +
342A GLY 3.8 13.2 + - - +
343A GLY* 4.3 1.3 - - - -
344A GLU 3.2 18.6 - - - -
345A VAL* 3.5 20.4 - - + -
385A PHE* 5.9 0.2 - + - -
387A ASN* 3.0 35.1 + - - -
442A LEU* 6.0 1.1 - - + -
444A GLY* 5.6 2.9 - - - -
445A PRO* 5.3 4.7 - - + +
448A TRP* 5.0 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A PRO* 5.9 2.9 - - + +
339A TYR* 3.8 31.6 - - + -
340A TYR* 1.3 75.7 - - - +
342A GLY* 1.3 64.0 + - - +
343A GLY 3.0 8.8 + - - -
344A GLU* 3.1 25.9 + - - +
346A PHE* 4.2 17.3 - - + -
----------------------------------------------------------
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