Contacts of the strand formed by residues 338 - 344 (chain A) in PDB entry 4XX1
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 GLY 338 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A TYR* 3.6 2.4 - - - -
326A ILE* 2.8 48.4 + - - +
336A PRO* 3.3 3.1 - - - +
337A VAL* 1.3 82.4 - - - +
339A VAL* 1.3 68.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A PRO* 3.8 22.4 - - + -
324A THR 3.5 6.7 - - - +
325A TYR* 4.0 20.4 - - + -
326A ILE* 4.9 0.2 - - - +
336A PRO* 5.0 7.4 - - + +
337A VAL 5.7 0.2 - - - -
338A GLY* 1.3 80.4 - - - +
340A LEU* 1.3 76.1 + - - +
341A TYR* 3.1 43.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A PRO* 3.4 0.9 - - - +
323A ARG* 3.0 66.4 + - + +
324A THR* 3.1 25.6 + - + +
326A ILE* 4.5 14.1 - - + -
338A GLY 4.4 0.2 - - - -
339A VAL* 1.3 88.5 - - - +
341A TYR* 1.3 60.8 + - - +
502A NAG 3.8 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A PRO* 3.3 47.6 - - + -
321A THR 3.3 12.8 - - - +
322A PRO* 3.7 15.0 - - + +
323A ARG* 3.1 23.6 + - - +
339A VAL* 3.1 48.2 - - + +
340A LEU* 1.3 79.2 - - - +
342A GLU* 1.3 61.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A TRP* 3.2 23.3 + - - -
320A PRO* 3.8 2.6 - - - -
321A THR* 2.7 40.4 + - - +
322A PRO 4.5 2.4 - - - +
323A ARG* 3.7 25.3 - - + +
341A TYR* 1.3 75.9 - - - +
343A ASP* 1.3 67.5 + - - +
344A GLY 3.2 0.2 + - - -
349A ALA* 3.6 19.9 - - + +
351A ARG* 2.9 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A VAL* 4.9 2.4 - - - +
318A GLY* 2.7 38.1 + - - -
319A LEU 4.2 2.9 - - - -
320A PRO* 5.5 0.2 - - - -
321A THR* 4.3 0.7 - - - -
342A GLU* 1.3 75.1 - - - +
344A GLY* 1.3 60.2 + - - +
349A ALA* 3.7 4.7 - - - +
350A THR* 2.9 38.2 + - + +
351A ARG 4.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A GLY 3.8 4.5 - - - -
317A VAL* 3.2 15.6 - - - -
318A GLY 3.3 0.2 + - - -
319A LEU 3.0 26.8 + - - -
321A THR* 3.1 13.2 - - - -
342A GLU 3.2 1.8 + - - -
343A ASP* 1.3 76.4 + - - +
345A ASP* 1.3 59.7 + - - -
348A VAL 3.3 13.2 - - - -
349A ALA* 4.0 0.4 - - - -
350A THR* 3.9 7.4 - - - -
----------------------------------------------------------
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