Contacts of the helix formed by residues 343 - 349 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ALA* 3.9 7.9 - - - +
32B MET* 3.4 24.9 - - - +
342B TYR* 1.3 69.8 - - - +
344B ARG* 1.3 67.9 + - - +
345B LEU 3.2 1.3 - - - -
346B PHE* 2.8 19.4 + - - +
347B ILE 3.3 6.8 + - - -
403B FMN 2.5 26.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 344 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B MET* 4.0 1.8 - - - -
322B GLY* 4.8 5.5 - - - +
343B GLY* 1.3 70.1 - - - -
345B LEU* 1.3 63.1 + - + +
347B ILE* 3.1 26.3 + - - +
348B ALA 3.5 3.5 + - - -
365B TYR* 3.5 58.4 + - + -
367B ARG* 4.9 11.5 - - - +
370B PHE* 3.9 15.9 - - + -
403B FMN 2.5 74.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 345 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B PHE 4.2 19.1 - - - +
324B ASN* 4.3 17.5 - - + -
342B TYR* 4.5 10.5 - - + -
343B GLY 3.0 1.6 + - - +
344B ARG* 1.3 79.0 - - + +
346B PHE* 1.3 57.2 + - - +
348B ALA 3.4 0.7 + - - -
349B ASN* 2.9 45.1 + - - +
352B LEU* 3.8 16.4 - - + -
356B PHE* 4.5 7.4 - - + -
362B LEU* 3.8 32.5 - - + -
363B ASN 5.0 3.8 - - - +
365B TYR* 5.0 11.9 - - + -
403B FMN 5.1 1.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 346 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B VAL* 4.2 9.6 - - + -
28B VAL* 4.0 6.1 - - - -
29B LEU* 3.8 43.3 - - + -
32B MET* 4.5 0.9 - - + -
53B ARG* 3.0 56.2 + - + -
60B LEU* 5.2 1.1 - - + -
342B TYR* 3.6 19.5 + - + +
343B GLY 2.8 11.6 + - - +
345B LEU* 1.3 76.0 - - - +
347B ILE* 1.3 64.2 + - - +
349B ASN 3.5 16.8 + - - +
350B PRO 3.4 22.0 - - - -
352B LEU* 3.8 29.0 - - + +
353B VAL* 4.6 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 347 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B MET* 3.6 34.3 - - + +
34B ARG* 3.7 32.0 + - - +
49B TYR* 4.6 1.6 - - - +
53B ARG* 2.7 26.8 + - - +
343B GLY 3.3 0.2 + - - -
344B ARG* 3.1 16.5 + - - +
346B PHE* 1.3 77.6 - - - +
348B ALA* 1.3 58.4 + - - +
365B TYR* 4.4 3.8 - - + -
370B PHE* 3.7 42.8 - - + -
379B TYR 4.9 0.2 - - - +
382B TYR* 3.3 30.5 - - + +
403B FMN 4.2 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 348 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B ARG 3.5 2.1 + - - +
345B LEU 3.4 2.5 + - - +
347B ILE* 1.3 79.1 - - - +
349B ASN* 1.3 62.0 + - - +
350B PRO* 3.6 2.6 - - - +
363B ASN* 2.9 53.5 + - - +
365B TYR* 3.8 28.7 - - + +
382B TYR* 3.4 26.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 349 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B LEU* 2.9 29.7 + - - +
346B PHE* 3.5 11.1 - - - +
347B ILE 3.4 1.0 - - - -
348B ALA* 1.3 83.7 - - - +
350B PRO* 1.3 61.9 - - - +
351B ASP* 3.1 3.4 - - - -
352B LEU* 2.9 32.3 + - + +
355B ARG* 3.3 33.1 + - - +
362B LEU* 3.5 12.4 - - - +
363B ASN* 2.8 45.6 + - - +
----------------------------------------------------------
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