Contacts of the helix formed by residues 343 - 349 (chain A) in PDB entry 2G5W
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 343 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ALA* 3.9 7.2 - - - +
32A MET* 3.2 37.0 - - - +
342A TYR* 1.3 71.8 - - - +
344A ARG* 1.3 64.5 + - - -
345A LEU 3.3 1.3 - - - +
346A PHE* 3.0 13.2 + - - +
347A ILE 3.3 2.3 + - - -
401A FMN 2.6 26.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A MET* 4.1 0.2 - - - -
284A ARG* 5.3 6.9 - - - +
322A GLY* 4.2 13.3 - - - +
343A GLY* 1.3 70.7 - - - +
345A LEU* 1.3 62.7 + - + +
347A ILE* 3.4 25.3 + - - +
348A ALA* 3.5 4.7 + - - +
365A TYR* 3.4 59.0 + - + +
367A ARG* 4.5 11.5 - - - +
370A PHE* 4.4 6.5 - - + -
401A FMN 2.7 60.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A PHE 3.7 22.9 - - - +
324A ASN* 4.3 13.9 - - + -
342A TYR* 4.3 13.2 - - + -
343A GLY 3.3 1.4 - - - +
344A ARG* 1.3 81.4 - - + +
346A PHE* 1.3 57.7 + - - +
348A ALA* 3.5 1.1 + - - -
349A ASN* 2.8 46.6 + - - +
352A LEU* 4.0 15.7 - - + +
356A PHE* 4.4 9.6 - - + -
362A LEU* 3.9 31.0 - - + -
363A ASN 5.0 3.1 - - - +
365A TYR* 5.1 10.3 - - + -
401A FMN 5.1 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A VAL* 4.0 17.9 - - + -
28A VAL 3.8 6.3 - - - -
29A LEU* 3.7 47.8 - - + -
32A MET* 4.9 1.3 - - - -
53A ARG* 3.0 61.4 + - + -
60A LEU* 5.1 2.5 - - + -
342A TYR* 3.6 19.9 - - + +
343A GLY 3.0 5.2 + - - +
345A LEU* 1.3 75.9 - - - +
347A ILE* 1.3 64.1 + - - +
349A ASN 3.5 16.4 + - - +
350A PRO 3.8 12.8 - - - -
352A LEU* 3.7 19.6 - - + +
353A VAL* 4.1 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A MET* 3.6 35.0 - - + -
34A ARG* 3.5 42.0 - - - +
49A TYR* 4.8 0.9 - - - +
53A ARG* 2.9 28.7 + - - +
343A GLY 3.3 4.1 + - - +
344A ARG* 3.5 11.7 - - - +
345A LEU 3.3 0.4 - - - -
346A PHE* 1.3 76.1 - - - +
348A ALA* 1.3 61.4 + - - +
365A TYR* 4.9 1.1 - - + -
370A PHE* 3.9 36.1 - - + -
382A TYR* 3.2 32.6 - - + +
401A FMN 4.4 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 348 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A ARG 3.5 2.6 + - - +
345A LEU* 3.5 3.7 + - - +
346A PHE 3.4 0.2 - - - -
347A ILE* 1.3 80.8 - - - +
349A ASN* 1.3 64.1 + - - +
350A PRO* 3.6 1.3 - - - +
363A ASN* 3.2 49.0 + - - +
364A LYS 3.7 5.8 - - - +
365A TYR* 3.6 28.5 - - + +
382A TYR* 3.4 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A LEU* 2.8 30.6 + - - +
346A PHE* 3.5 12.1 - - - +
347A ILE 3.2 1.2 - - - -
348A ALA* 1.3 82.4 - - - +
350A PRO* 1.3 65.6 - - - +
351A ASP 3.1 2.0 - - - +
352A LEU* 3.0 24.5 + - + +
355A ARG* 3.3 38.1 + - - +
362A LEU* 3.4 12.1 - - - +
363A ASN* 2.8 44.9 + - - +
----------------------------------------------------------
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