Contacts of the helix formed by residues 348 - 356 (chain A) in PDB entry 6F3T
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 SER 348 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ALA* 5.4 0.4 - - - -
346A PRO 3.7 1.6 + - - -
347A ARG* 1.3 77.7 - - - +
349A LYS* 1.3 65.0 + - - +
350A GLN* 3.6 9.5 + - - +
351A GLN* 3.2 36.1 + - - +
352A ILE* 3.0 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ALA* 4.2 28.3 + - + +
237A SER* 3.4 21.4 + - - -
238A GLN* 6.0 0.4 - - - +
272A GLU* 2.8 29.7 + - - -
274A TYR* 4.7 1.2 + - - -
348A SER* 1.3 74.9 - - - +
350A GLN* 1.3 57.2 + - - +
352A ILE* 4.4 10.5 - - + +
353A ASP* 2.9 56.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A SER* 3.1 9.3 + - - +
349A LYS* 1.3 79.7 - - - +
351A GLN* 1.3 65.8 + - + +
353A ASP* 3.4 4.3 + - - +
354A ALA* 3.2 24.4 + - + +
706A GLU* 5.6 3.9 - - - +
708A LYS* 5.9 0.4 - - - +
761A LEU* 3.5 24.3 - - - +
762A PRO 5.1 0.2 - - - -
763A GLU* 3.1 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A ARG* 4.1 18.0 + - + +
348A SER* 3.2 32.7 + - - +
350A GLN* 1.3 84.0 - - + +
352A ILE* 1.3 66.2 + - - +
354A ALA* 3.4 5.6 + - - +
355A MET* 3.3 25.7 + - + +
758A HIS* 3.6 23.8 + - + +
759A ILE 3.3 27.6 + - - +
760A ASN* 3.0 31.0 + - - +
761A LEU* 4.9 6.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ALA* 3.5 33.4 - - + +
235A GLU* 3.9 13.5 - - + -
238A GLN* 3.7 29.4 - - + +
274A TYR* 5.3 0.2 - - - +
347A ARG* 3.7 45.1 - - + +
348A SER 3.0 20.8 + - - +
349A LYS* 3.8 10.5 - - + +
351A GLN* 1.3 76.2 - - - +
353A ASP* 1.3 71.0 + - - +
355A MET* 3.0 12.6 + - - -
356A VAL* 3.0 22.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A GLU* 4.5 1.6 - - - +
274A TYR* 2.7 36.5 + - + +
349A LYS* 2.9 52.5 + - - +
350A GLN* 4.0 4.8 - - - +
351A GLN 3.4 0.2 - - - -
352A ILE* 1.3 78.6 - - - +
354A ALA* 1.3 52.1 + - - +
355A MET 3.5 0.3 + - - -
356A VAL* 3.8 4.9 - - - +
669A LYS* 2.6 36.4 + - - -
692A ARG* 5.0 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A GLN* 3.2 18.0 + - + +
351A GLN* 3.8 7.4 - - - +
352A ILE 3.1 1.0 - - - -
353A ASP* 1.3 78.1 - - - +
355A MET* 1.3 59.5 + - + +
667A GLY* 3.2 23.7 - - - +
692A ARG* 3.8 10.9 + - - +
703A MET* 3.3 26.6 - - - +
706A GLU* 3.8 21.5 - - - +
761A LEU* 4.8 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A ARG* 3.8 14.1 - - - +
351A GLN* 3.3 15.0 + - + +
352A ILE 3.0 3.4 + - - +
354A ALA* 1.3 79.6 - - + +
356A VAL* 1.3 60.7 + - - +
362A GLU* 3.7 23.2 - - + +
363A ALA 6.0 0.4 - - - +
665A PHE* 6.0 0.2 - - - -
666A THR* 3.0 64.8 + - - +
667A GLY* 3.8 0.9 - - - -
696A TRP* 4.6 4.0 - - + -
703A MET* 3.7 39.7 - - + +
757A GLY 5.8 5.8 - - - +
758A HIS* 5.5 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A GLN* 3.5 29.2 - - + +
274A TYR* 3.4 33.0 - - + +
275A TYR* 4.2 7.4 - - - +
352A ILE* 3.0 26.6 + - + +
353A ASP* 4.0 4.5 - - - +
355A MET* 1.3 78.1 - - - +
357A GLY* 1.3 61.3 + - - +
358A SER 3.8 1.3 - - - -
361A GLY 6.2 0.4 - - - -
362A GLU* 3.8 21.8 - - + +
666A THR* 5.5 0.9 - - - -
667A GLY* 3.2 10.7 - - - +
669A LYS* 2.9 22.0 + - - -
----------------------------------------------------------
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