Contacts of the helix formed by residues 52 - 62 (chain B) in PDB entry 1GQC
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 ASP 52 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B TYR* 3.5 29.4 - - + +
50B THR* 3.3 6.3 + - - +
51B ASP* 1.3 84.0 + - - +
53B PRO* 1.3 73.1 - - - +
54B ARG* 2.7 70.1 + - - +
55B VAL* 3.1 16.2 + - + +
56B GLU* 3.2 9.4 + - - +
68B MET* 4.3 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ASP 4.2 3.8 - - - +
52B ASP* 1.3 96.8 - - - +
54B ARG* 1.3 57.0 + - + +
55B VAL 3.4 0.2 - - - -
56B GLU* 3.6 16.6 - - + +
57B GLN* 2.9 39.9 + - + +
68B MET* 4.5 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B TYR* 3.2 46.8 + - + -
21B LEU* 4.3 17.7 - - + +
52B ASP* 2.7 46.7 + - - +
53B PRO* 1.3 71.6 - - + +
55B VAL* 1.3 61.9 + - - +
57B GLN* 3.4 8.2 + - - +
58B ALA* 3.1 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ALA* 4.0 15.9 - - + +
11B TYR* 4.2 27.6 - - + -
20B PRO* 4.1 20.6 - - + -
21B LEU* 4.2 13.0 - - + -
30B ILE* 5.3 2.5 - - + -
48B VAL* 4.5 6.3 - - + -
50B THR* 3.0 39.7 - - + +
52B ASP* 3.1 3.6 + - + +
54B ARG* 1.3 73.1 - - - +
56B GLU* 1.3 65.5 + - - +
58B ALA* 3.1 3.3 + - - +
59B VAL* 2.9 36.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B THR* 3.8 9.1 - - + +
52B ASP 3.2 8.7 + - - +
53B PRO* 3.6 12.9 - - - +
55B VAL* 1.3 81.0 - - - +
57B GLN* 1.3 72.3 + - - +
59B VAL* 3.5 1.4 + - - +
60B GLN* 3.0 53.0 + - - +
66B ALA* 4.2 20.9 - - + +
68B MET* 3.5 37.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B PRO* 2.9 34.7 + - + +
54B ARG* 3.7 7.6 - - - +
55B VAL 3.2 0.2 - - - -
56B GLU* 1.3 85.9 + - - +
58B ALA* 1.3 62.7 + - - +
60B GLN* 3.2 19.1 + - - +
61B ALA* 2.9 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU* 3.5 26.0 - - + -
28B PRO* 5.5 6.1 - - + -
30B ILE* 5.4 4.7 - - + -
54B ARG 3.1 15.0 + - - +
55B VAL 3.1 3.3 + - - +
57B GLN* 1.3 81.2 - - - +
59B VAL* 1.3 61.0 + - + +
61B ALA* 3.5 12.8 + - - +
62B PHE* 3.1 22.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ILE* 4.3 14.6 - - + -
48B VAL* 3.8 35.0 - - + -
55B VAL* 2.9 23.7 + - + +
56B GLU 3.8 4.5 - - - +
58B ALA* 1.3 78.0 - - - +
60B GLN* 1.3 61.0 + - - +
61B ALA 3.5 0.2 + - - -
62B PHE* 3.6 17.7 - - + -
64B GLY* 2.7 50.0 + - - -
65B LYS 3.6 19.3 - - - +
66B ALA* 3.8 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B GLU* 3.0 38.2 + - + +
57B GLN* 3.7 22.6 + - - +
59B VAL* 1.3 76.5 - - - +
61B ALA* 1.3 64.9 + - - +
63B GLY* 3.1 12.6 + - - -
64B GLY 3.7 13.5 - - - +
65B LYS* 5.9 0.2 - - - -
66B ALA* 4.8 13.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B GLN 2.9 16.9 + - - +
58B ALA* 3.8 9.2 - - - +
59B VAL 3.3 0.6 - - - -
60B GLN* 1.3 78.1 - - - +
62B PHE* 1.3 57.7 + - - +
63B GLY 3.2 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B PRO* 4.9 5.2 - - + -
30B ILE* 4.4 9.0 - - + -
31B GLN* 3.5 68.0 - - + +
34B TYR* 3.7 31.0 - + + -
35B GLU* 5.5 3.4 - - + -
58B ALA 3.1 25.3 + - - +
59B VAL* 3.6 25.4 - - + -
60B GLN 3.2 0.2 - - - -
61B ALA* 1.3 77.7 - - + +
63B GLY* 1.3 56.0 + - - +
64B GLY* 3.5 11.7 - - - -
----------------------------------------------------------
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