Contacts of the helix formed by residues 102 - 122 (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 PRO 102 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100J LYS 3.0 12.8 - - - +
101J ILE* 1.3 85.5 - - - +
103J ASP* 1.3 56.6 + - - +
104J ASN* 2.7 26.6 + - + +
105J TYR* 2.9 57.7 + - + +
106J PHE* 3.7 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 103 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101J ILE 4.6 3.8 - - - +
102J PRO* 1.3 70.6 - - - +
104J ASN* 1.3 61.8 + - - +
105J TYR 3.4 0.2 - - - -
106J PHE* 4.0 10.8 - - - +
107J ASP* 3.2 22.5 + - - +
142J LYS* 3.6 34.8 + - - +
144J HIS* 3.8 28.7 + - - +
145J HIS* 4.5 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 104 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41J VAL* 4.2 13.9 - - - +
43J GLU* 6.3 0.2 - - - +
102J PRO* 2.7 14.9 + - + +
103J ASP* 1.3 78.9 - - - +
105J TYR* 1.3 87.7 + - - +
107J ASP* 3.2 19.0 - - - +
108J ALA* 3.4 7.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 105 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37J THR* 5.4 1.3 - - + +
41J VAL* 4.0 19.2 - - + +
43J GLU* 3.3 28.5 + - + +
44J SER* 3.3 27.4 + - - -
47J LEU* 3.9 19.0 - - + +
100J LYS 5.2 0.2 - - - -
101J ILE* 4.1 1.6 - - + -
102J PRO* 2.9 36.3 + - + +
104J ASN* 1.3 93.2 - - - +
106J PHE* 1.3 67.8 + - - +
107J ASP 3.0 1.3 - - - -
108J ALA* 2.8 19.7 + - - +
109J PHE* 2.9 12.3 + - - +
160J HEM 3.6 39.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 106 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96J HIS* 4.8 3.6 - + + -
101J ILE* 3.3 42.6 - - + -
102J PRO 3.9 8.1 - - - -
103J ASP* 3.7 7.2 + - - +
104J ASN 3.5 0.2 - - - -
105J TYR* 1.3 77.2 - - - +
107J ASP* 1.3 62.8 + - - +
109J PHE* 3.2 1.0 + - - +
110J LYS* 2.9 12.5 + - - +
138J GLU* 2.8 50.1 - - + +
141J ILE* 4.3 25.4 - - + -
142J LYS* 3.8 42.6 - - + +
160J HEM 3.7 37.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 107 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103J ASP 3.2 12.1 + - - +
104J ASN* 3.2 15.0 - - - +
105J TYR 3.0 0.4 - - - -
106J PHE* 1.3 77.8 - - - +
108J ALA* 1.3 63.9 + - - +
110J LYS* 3.1 25.3 + - - +
111J THR* 3.0 28.9 + - - -
138J GLU* 4.9 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 108 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37J THR* 4.4 4.3 - - + +
40J GLN* 3.0 45.9 - - + +
41J VAL* 4.0 25.4 - - + -
104J ASN 3.4 3.7 + - - +
105J TYR 2.8 12.4 + - - +
107J ASP* 1.3 76.0 + - - +
109J PHE* 1.3 52.4 + - - +
111J THR* 3.1 1.6 + - - -
112J ALA* 2.7 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 109 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33J ILE* 4.2 13.5 - - + -
34J TRP* 3.4 41.7 - + - -
37J THR* 3.4 24.8 + - + +
68J VAL* 4.2 19.1 - - + -
69J LEU* 5.4 6.1 - - + -
72J LEU* 5.1 3.6 - - + -
105J TYR 2.9 10.8 + - - +
106J PHE 3.6 7.4 - - - +
108J ALA* 1.3 77.8 - - - +
110J LYS* 1.3 62.2 + - - +
112J ALA* 3.4 1.7 + - - +
113J ILE* 3.0 53.6 + - + +
138J GLU* 4.3 4.5 - - - -
160J HEM 3.5 47.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 110 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106J PHE 2.9 13.1 + - - +
107J ASP* 3.3 26.2 + - - +
109J PHE* 1.3 71.9 - - - +
111J THR* 1.3 75.1 + - - +
113J ILE* 3.0 7.2 + - - +
114J LEU* 2.8 33.3 + - + +
131J ASP* 3.5 33.2 + - - +
134J ILE* 3.3 33.4 - - + -
135J ASP* 3.0 28.4 + - - +
138J GLU* 3.7 14.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 111 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40J GLN* 3.7 23.8 + - - +
107J ASP* 3.0 15.9 + - - -
108J ALA 3.1 8.0 + - - -
110J LYS* 1.3 86.2 - - - +
112J ALA* 1.3 66.9 + - - +
114J LEU* 3.1 8.7 + - - +
115J HIS* 2.9 49.4 + - + +
127J ARG* 6.3 0.7 - - - +
137O PHE* 3.8 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 112 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33J ILE* 3.4 18.8 - - + +
36J ALA* 3.8 12.6 - - + -
37J THR* 3.2 35.9 - - - +
40J GLN* 3.9 2.8 + - - +
108J ALA 2.7 12.9 + - - +
109J PHE 3.4 5.8 - - - +
111J THR* 1.3 76.0 - - - +
113J ILE* 1.3 65.6 + - - +
115J HIS* 3.0 3.4 + - - +
116J VAL* 2.9 26.7 + - - +
137O PHE* 5.8 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 113 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16J TRP* 5.1 1.6 - - + -
33J ILE* 3.9 27.7 - - + +
72J LEU* 3.5 26.7 - - + -
109J PHE* 3.0 45.3 + - + +
110J LYS* 3.3 8.7 - - - +
112J ALA* 1.3 78.6 - - - +
114J LEU* 1.3 71.1 + - + +
116J VAL* 3.2 1.0 + - - +
117J VAL* 2.8 49.5 + - + +
130J TRP* 4.3 10.8 - - + -
134J ILE* 4.2 16.4 - - + -
160J HEM 5.5 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 114 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110J LYS* 2.8 30.6 + - + +
111J THR* 3.5 10.8 - - - +
113J ILE* 1.3 77.4 - - + +
115J HIS* 1.3 61.9 + - + +
117J VAL* 3.7 3.4 - - - +
118J ALA* 2.9 31.8 + - - +
125J TYR* 3.6 22.2 + - - +
127J ARG* 4.5 21.8 - - + +
130J TRP* 4.1 15.5 - - + -
131J ASP* 4.1 33.4 - - + +
134J ILE* 4.0 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 115 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36J ALA* 5.9 1.3 - - + -
111J THR* 2.9 45.4 + - + +
112J ALA* 3.6 7.4 - - - +
114J LEU* 1.3 75.8 - - + +
116J VAL* 1.3 64.3 + - + +
118J ALA* 3.4 6.8 + - - +
119J ALA* 3.0 22.3 + - - +
127J ARG* 5.5 11.0 - - - -
135O ALA* 4.3 14.9 - - + +
137O PHE* 3.8 25.0 - + + -
138O PHE* 3.6 25.7 - + + -
143O ASP* 5.6 6.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 116 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29J PHE* 3.7 32.5 - - + +
32J ALA* 3.9 17.7 - - + +
33J ILE* 3.7 39.7 - - + +
36J ALA* 4.7 3.8 - - + -
112J ALA 2.9 16.1 + - - +
113J ILE 3.7 1.8 - - - +
115J HIS* 1.3 74.3 - - + +
117J VAL* 1.3 67.6 - - - +
119J ALA* 2.8 13.9 + - - +
120J GLN* 2.8 16.5 + - + +
80O LEU* 4.6 6.7 - - + -
138O PHE* 4.1 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 117 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19J ALA* 4.0 3.8 - - + -
29J PHE* 3.8 28.7 - - + -
113J ILE* 2.8 31.5 + - + +
114J LEU* 3.7 3.6 - - - +
116J VAL* 1.3 70.2 - - - +
118J ALA* 1.3 58.4 + - - +
120J GLN* 3.0 3.5 + - - -
121J LEU* 2.8 52.1 + - + +
125J TYR* 3.6 18.2 - - + -
130J TRP* 3.7 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 118 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114J LEU 2.9 18.3 + - - +
115J HIS* 3.6 7.2 - - - +
117J VAL* 1.3 76.4 - - - +
119J ALA* 1.3 63.3 + - - +
121J LEU* 4.1 1.0 - - - +
122J GLY* 3.3 25.3 + - - +
125J TYR* 3.9 33.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 119 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115J HIS 3.0 13.3 + - - +
116J VAL* 2.8 12.6 + - - +
118J ALA* 1.3 74.7 - - - +
120J GLN* 1.3 61.6 + - - +
122J GLY* 3.9 5.9 + - - -
80O LEU* 4.3 11.8 - - + +
138O PHE* 3.5 25.6 - - + -
141O ILE* 4.3 20.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 120 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18J ARG 4.8 2.1 - - - +
19J ALA* 3.3 29.5 - - + +
25J ASP* 4.6 14.5 + - - +
29J PHE* 3.9 21.6 - - + +
116J VAL* 2.8 10.6 + - + +
117J VAL* 3.5 9.9 - - - +
119J ALA* 1.3 80.3 - - - +
121J LEU* 1.3 62.4 + - - +
122J GLY 3.3 0.7 + - - -
65O HIS* 4.5 32.3 + - - +
80O LEU* 4.2 30.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 121 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15J GLU* 3.8 29.2 - - + +
18J ARG* 3.7 29.4 + - + +
19J ALA* 3.6 31.2 - - + +
117J VAL* 2.8 39.9 + - + +
118J ALA 4.5 0.9 - - - +
120J GLN* 1.3 74.3 - - - +
122J GLY* 1.3 58.2 + - - +
123J ARG* 2.8 26.3 + - - -
124J CYS 3.7 19.9 + - - +
125J TYR* 3.9 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 122 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118J ALA 3.3 16.5 + - - +
119J ALA 3.9 5.0 + - - -
120J GLN 3.3 4.9 + - - -
121J LEU* 1.3 74.2 - - - +
123J ARG* 1.3 63.2 + - - -
125J TYR* 5.8 1.4 - - - +
168O GLU* 4.3 10.3 - - - +
177O THR* 5.9 3.6 - - - -
179O HIS* 3.7 14.0 + - - -
----------------------------------------------------------
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