Contacts of the helix formed by residues 81 - 97 (chain J) in PDB entry 2GTL
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 GLN 81 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29I ASP* 6.0 0.2 - - - +
77J SER 4.2 2.6 + - - -
78J THR* 3.0 16.3 + - - +
80J ASP* 1.3 101.3 + - - +
82J PRO* 1.3 71.6 - - - -
83J ALA* 2.8 6.8 + - + -
84J THR* 2.9 30.6 + - - +
85J LEU 3.0 8.8 + - - -
29K SER* 3.2 33.5 + - - -
30K LYS* 3.8 24.7 + - - +
33K ILE* 4.1 14.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 82 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78J THR 4.2 0.6 - - - +
79J LEU 4.9 4.0 - - - +
80J ASP* 3.7 7.4 - - - +
81J GLN* 1.3 85.5 - - - +
83J ALA* 1.3 68.2 + - + +
85J LEU* 3.9 11.8 - - + +
86J LYS* 2.9 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 83 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81J GLN* 2.8 6.4 + - + +
82J PRO* 1.3 83.3 - - + +
84J THR* 1.3 63.6 + - - +
86J LYS* 3.2 15.9 - - - +
87J GLU* 3.6 5.2 + - - +
65K PRO* 3.6 29.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 84 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74J ILE* 6.2 0.2 - - + -
78J THR* 4.7 14.6 - - + -
81J GLN* 2.9 31.4 + - - +
83J ALA* 1.3 72.1 - - - +
85J LEU* 1.3 68.6 + - - +
87J GLU* 2.7 17.0 + - - +
88J GLU* 3.1 10.4 + - + +
33K ILE* 4.9 2.9 - - + -
65K PRO* 3.7 17.6 - - - +
68K SER* 4.0 12.3 - - - +
69K ALA* 3.6 35.0 - - + +
72K LEU* 4.8 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 85 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75J ALA* 3.5 32.8 - - + +
78J THR* 3.4 29.0 + - - +
79J LEU* 3.9 25.8 - - + +
81J GLN 3.0 7.7 + - - +
82J PRO* 3.9 9.2 - - + +
84J THR* 1.3 76.6 - - - +
86J LYS* 1.3 66.6 + - - +
88J GLU* 2.9 6.9 + - + +
89J LEU* 2.8 60.0 + - + +
136J HIS* 4.2 18.2 - - + +
137J ILE* 5.2 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 86 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82J PRO 2.9 20.4 + - - +
83J ALA* 3.2 9.2 - - - +
85J LEU* 1.3 78.2 - - - +
87J GLU* 1.3 67.2 + - - +
89J LEU* 3.4 7.3 + - - +
90J ASP* 2.9 61.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 87 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83J ALA 3.6 8.4 + - - +
84J THR* 2.7 17.4 + - - +
86J LYS* 1.3 83.5 - - - +
88J GLU* 1.3 57.7 + - - +
90J ASP* 3.0 13.8 + - - +
91J HIS* 2.8 29.6 + - - +
65K PRO* 4.4 7.5 - - - +
66K LYS* 3.1 61.0 + - + +
69K ALA* 3.9 13.9 - - + -
73K ARG* 5.3 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 88 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71J GLY* 4.3 4.4 - - - +
74J ILE* 3.5 43.9 - - + +
75J ALA* 4.3 10.3 - - - +
84J THR* 3.1 6.7 + - + +
85J LEU* 2.9 15.6 + - + +
87J GLU* 1.3 75.2 - - - +
89J LEU* 1.3 66.0 + - - +
91J HIS* 3.0 9.9 + - - +
92J LEU* 2.9 55.1 + - + +
95J GLN* 5.4 0.2 + - - -
69K ALA* 4.2 8.7 - - + +
73K ARG* 3.0 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 89 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75J ALA* 4.4 4.9 - - + -
85J LEU* 2.8 57.0 + - + +
86J LYS* 3.6 7.0 - - - +
88J GLU* 1.3 71.9 - - - +
90J ASP* 1.3 54.5 + - - +
92J LEU* 2.9 10.8 + - + +
93J GLN* 2.7 33.8 + - - +
136J HIS* 4.6 14.6 - - + +
137J ILE* 3.3 44.6 - - + +
140J GLY* 3.7 25.6 - - - +
141J ILE* 4.1 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 90 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86J LYS* 2.9 47.9 + - - +
87J GLU* 3.3 18.0 - - - +
89J LEU* 1.3 76.4 - - - +
91J HIS* 1.3 65.2 + - - +
93J GLN* 3.1 37.0 + - - +
94J VAL* 3.2 13.4 + - - +
140J GLY 4.7 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 91 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87J GLU 2.8 15.2 + - - +
88J GLU* 3.2 14.9 + - - +
90J ASP* 1.3 72.8 - - - +
92J LEU* 1.3 65.6 + - - +
94J VAL* 3.1 18.6 + - + +
95J GLN* 3.3 26.3 + - + +
56K ARG* 5.1 17.6 + - - -
73K ARG* 3.1 49.0 + - + +
160K HEM 3.3 43.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71J GLY* 4.8 8.7 - - - +
75J ALA* 5.3 2.5 - - + -
88J GLU* 2.9 41.5 + - + +
89J LEU* 3.3 14.4 - - + +
91J HIS* 1.3 71.8 - - - +
93J GLN* 1.3 68.9 + - - +
95J GLN* 2.7 36.7 + - - +
96J HIS* 3.1 18.3 + - + +
141J ILE* 3.6 35.0 - - + -
160J HEM 3.9 38.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 93 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89J LEU 2.7 15.4 + - - +
90J ASP* 3.1 28.5 + - - +
92J LEU* 1.3 71.2 - - - +
94J VAL* 1.3 60.9 + - - +
96J HIS* 3.3 2.3 + - - +
97J GLU* 2.9 37.2 + - + +
140J GLY* 3.6 16.9 + - - +
141J ILE* 3.4 27.8 - - - +
142J LYS 4.6 5.2 - - - +
143J GLY* 3.9 20.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 94 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90J ASP 3.4 14.4 - - - +
91J HIS* 3.1 12.3 + - + +
92J LEU 2.8 3.8 + - - -
93J GLN* 1.3 74.9 - - + +
95J GLN* 1.3 58.1 + - + +
96J HIS 2.7 14.9 + - - -
97J GLU* 3.3 37.6 + - - +
56K ARG* 6.3 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 95 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91J HIS* 3.4 39.2 + - + +
92J LEU* 2.7 34.0 + - - +
94J VAL* 1.3 73.1 - - + +
96J HIS* 1.3 66.0 + - + +
97J GLU 4.8 0.8 - - - +
99J ARG* 2.9 29.7 + - - +
160J HEM 3.4 40.6 - - + +
101K GLN* 4.8 1.6 + - - -
160K HEM 4.2 15.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 96 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92J LEU* 3.1 21.0 + - + +
93J GLN 3.8 6.1 - - - +
94J VAL 2.7 3.6 + - - -
95J GLN* 1.3 84.2 - - + +
97J GLU* 1.3 67.7 + - - +
99J ARG* 3.1 29.5 + - - +
101J ILE* 3.7 18.1 - - + +
106J PHE* 4.8 3.6 - + + -
141J ILE* 4.1 20.7 - - + +
160J HEM 1.9 94.4 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 97 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93J GLN* 2.9 25.9 + - + +
94J VAL* 3.4 35.7 - - - +
95J GLN 4.8 0.7 - - - +
96J HIS* 1.3 75.0 - - - +
98J GLY* 1.3 58.9 + - - +
99J ARG* 3.6 2.6 + - - +
141J ILE 5.5 0.4 + - - -
----------------------------------------------------------
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