Contacts of the strand formed by residues 338 - 345 (chain A) in PDB entry 2XHC
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 ARG 338 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A LEU 5.4 0.2 - - - -
232A PHE* 3.4 29.2 - - + +
233A PRO* 3.1 49.5 + - - +
235A TYR* 3.5 41.6 - - - +
333A VAL 3.1 10.4 - - - +
334A THR* 3.3 4.0 - - - +
335A ILE 2.5 26.4 + - - +
336A PHE* 3.3 13.2 - - - +
337A GLY* 1.3 73.9 - - - +
339A GLU* 1.3 62.0 + - - +
340A THR* 3.1 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A VAL* 6.0 0.3 - - - +
320A LYS* 4.7 4.3 + - - -
332A ASN* 2.9 44.6 + - - +
333A VAL 3.7 3.1 - - - +
334A THR* 3.7 15.7 + - - -
337A GLY 4.1 2.2 + - - -
338A ARG* 1.3 72.3 - - - +
340A THR* 1.3 59.9 + - - +
341A PRO* 4.0 7.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A LEU* 3.8 45.3 + - + +
232A PHE* 3.6 9.5 - - + -
312A PHE* 5.1 0.7 - - + -
332A ASN* 4.0 1.3 - - - -
333A VAL* 2.7 43.7 + - + +
335A ILE* 2.9 35.0 - - + +
338A ARG* 3.1 11.6 + - - +
339A GLU* 1.3 77.0 + - - +
341A PRO* 1.3 68.1 - - + +
342A VAL* 3.4 2.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLU* 3.8 4.0 - - - +
231A LEU* 3.7 19.2 - - + +
330A LYS* 4.1 24.2 - - + -
331A VAL 3.4 2.5 - - - +
332A ASN* 3.3 23.8 - - - +
339A GLU* 4.0 6.3 - - + +
340A THR* 1.3 85.6 - - + +
342A VAL* 1.3 60.2 + - - +
343A VAL* 5.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLU* 3.4 9.6 - - - +
231A LEU* 5.2 1.1 - - + -
307A ILE* 5.7 0.9 - - + -
312A PHE* 4.3 33.7 - - + -
330A LYS* 3.5 1.7 - - - +
331A VAL* 2.7 37.3 + - + +
333A VAL* 3.3 35.7 - - + -
340A THR* 3.4 4.9 - - + +
341A PRO* 1.3 74.0 - - - +
343A VAL* 1.3 74.6 + - - +
344A LEU* 3.2 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLU* 2.8 28.8 + - + +
45A VAL* 5.0 16.6 - - + -
209A ARG* 6.2 2.2 - - - +
328A GLU* 3.8 26.0 - - + +
329A LEU 3.3 7.4 - - - +
330A LYS* 4.6 23.6 - - + -
341A PRO 5.7 0.7 - - - +
342A VAL* 1.3 76.5 - - - +
344A LEU* 1.3 72.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A ILE* 3.5 38.6 - - + -
309A SER 5.5 0.4 - - - +
312A PHE* 5.4 1.8 - - + -
328A GLU* 3.5 6.8 - - - +
329A LEU* 2.9 45.6 + - + +
331A VAL* 3.4 17.3 - - + -
342A VAL* 3.2 28.7 - - + +
343A VAL* 1.3 79.8 - - - +
345A HIS* 1.3 68.8 + - - +
348A GLU* 3.4 17.9 - - + +
349A VAL* 4.2 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLY* 6.3 3.3 - - - -
209A ARG* 5.9 4.7 - - - -
326A ARG 4.8 2.5 - - - -
327A GLN* 3.4 9.6 - - + +
328A GLU* 3.4 30.7 + - - -
329A LEU* 4.9 1.1 - - - -
344A LEU* 1.3 77.7 - - - +
346A VAL* 1.3 58.0 + - + +
347A SER* 3.4 19.7 - - - +
348A GLU* 2.8 53.0 + - + +
349A VAL* 4.0 4.9 + - - +
----------------------------------------------------------
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