Contacts of the helix formed by residues 132 - 149 (chain K) 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 ASP 132 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E TYR* 4.1 13.8 - - - -
12E ARG* 2.8 34.4 + - - -
85E ASP* 4.7 9.9 - - - +
87E THR* 3.7 9.6 + - - +
14K ILE* 4.1 11.2 - - + -
18K GLN* 3.1 22.8 - - - +
131K TYR* 1.3 72.8 - - - +
133K ALA* 1.3 67.0 + - - +
134K LEU 3.7 1.2 + - - -
135K ALA* 2.9 37.7 + - + +
136K TRP* 3.1 14.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 133 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E THR* 3.5 21.8 + - - -
88E LEU* 4.9 9.4 - - + +
91E GLN* 4.4 16.6 - - - +
131K TYR* 3.4 30.9 + - + +
132K ASP* 1.3 70.6 - - - +
134K LEU* 1.3 64.6 + - + +
136K TRP* 3.4 0.5 + - - +
137K LYS* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 134 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E CYS* 4.5 20.0 - - + +
12E ARG* 3.5 44.9 - - - +
84E LEU* 4.9 2.2 - - + +
87E THR* 3.5 13.4 - - + +
90E LEU* 4.7 16.6 - - + -
141E ARG* 3.7 43.5 - - + +
132K ASP* 3.0 3.2 + - - +
133K ALA* 1.3 81.0 - - + +
135K ALA* 1.3 63.9 + - - +
137K LYS* 4.0 5.7 - - + +
138K SER* 3.0 27.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 135 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E TYR* 5.4 0.2 - - + -
12E ARG* 3.8 1.7 - - - +
11K ASP* 3.8 43.7 - - - +
14K ILE* 4.3 7.9 - - + -
15K VAL* 4.0 6.3 - - + -
132K ASP* 2.9 31.6 + - + +
134K LEU* 1.3 75.2 - - - +
136K TRP* 1.3 65.1 + - + +
138K SER* 3.2 4.3 + - - -
139K CYS* 3.1 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 136 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15K VAL* 3.6 51.5 - - + +
18K GLN* 2.7 30.3 - - - +
19K TRP* 3.6 40.2 - + + -
78K LEU* 5.8 1.1 - - + -
82K ILE* 4.1 13.0 - - + -
124K LEU* 3.3 23.3 - - + -
128K LEU* 4.2 10.5 - - + -
131K TYR* 3.3 39.7 - + + +
132K ASP* 3.1 12.1 + - + -
133K ALA 3.8 2.7 - - - +
135K ALA* 1.3 76.4 - - + +
137K LYS* 1.3 58.1 + - - +
139K CYS* 3.0 3.1 + - + +
140K LEU* 2.7 60.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 137 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141E ARG* 4.6 20.1 - - - +
121K ALA* 6.1 7.0 - - + -
131K TYR* 4.8 1.9 + - - +
133K ALA 2.9 21.9 + - - +
134K LEU* 4.0 6.1 - - + +
136K TRP* 1.3 72.7 - - - +
138K SER* 1.3 63.4 + - - +
140K LEU* 4.1 6.9 - - - +
141K LYS* 3.0 31.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 138 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E CYS* 4.4 13.3 - - - +
7E CYS 5.0 5.9 + - - -
6K CYS* 4.5 15.6 - - - +
7K CYS* 3.6 30.3 + - - +
11K ASP* 4.2 7.6 + - - -
134K LEU 3.0 16.4 + - - -
135K ALA 3.2 10.8 - - - -
136K TRP 3.1 0.6 - - - -
137K LYS* 1.3 82.1 - - - +
139K CYS* 1.3 60.7 + - - +
141K LYS* 3.6 5.3 - - - +
142K GLY* 3.5 13.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 139 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7K CYS* 2.0 53.1 - - - -
11K ASP 4.5 0.4 - - - -
12K HIS* 3.9 13.5 - - - -
15K VAL* 3.9 23.8 - - + -
85K LEU* 4.6 10.5 - - + -
135K ALA 3.1 11.3 + - - +
136K TRP 3.0 6.0 + - - +
138K SER* 1.3 76.2 - - - +
140K LEU* 1.3 69.8 + - + +
141K LYS 3.1 1.7 + - - -
142K GLY* 3.1 3.7 + - - -
143K ILE* 3.1 28.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 140 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78K LEU* 4.2 17.9 - - + -
82K ILE* 5.7 0.9 - - + -
117K GLY* 5.1 2.0 - - - +
120K LEU* 3.8 37.5 - - + -
121K ALA* 4.9 12.1 - - + +
124K LEU* 4.0 9.6 - - + -
131K TYR* 5.1 0.4 - - - +
136K TRP* 2.7 58.2 + - + +
137K LYS* 4.1 4.7 - - - +
139K CYS* 1.3 73.0 - - + +
141K LYS* 1.3 57.1 + - - +
143K ILE* 3.2 10.5 + - + +
144K LEU* 2.8 48.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 141 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E ASP* 5.8 1.8 + - - -
6K CYS* 5.2 14.8 - - - -
137K LYS* 3.0 25.0 + - + +
138K SER* 3.6 7.4 - - - +
140K LEU* 1.3 76.2 - - - +
142K GLY* 1.3 67.4 + - - +
143K ILE 3.0 0.5 + - - -
144K LEU* 3.9 4.9 - - - +
145K THR* 2.9 39.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 142 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7K CYS* 6.2 1.1 - - - -
95K LEU* 5.4 0.2 - - - -
138K SER 3.5 6.6 + - - -
139K CYS* 3.1 6.9 + - - -
141K LYS* 1.3 80.5 - - - +
143K ILE* 1.3 61.6 + - - +
145K THR* 3.9 4.4 - - - -
146K LYS* 3.2 39.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 143 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78K LEU* 4.7 9.4 - - + -
81K ALA* 3.8 27.1 - - + -
82K ILE* 4.5 12.8 - - + +
85K LEU* 4.5 22.9 - - + -
91K LEU* 5.4 1.1 - - + -
95K LEU* 3.6 33.4 - - + -
139K CYS* 3.1 19.8 + - + +
140K LEU* 3.5 13.0 - - + +
142K GLY* 1.3 74.1 - - - +
144K LEU* 1.3 69.2 + - + +
145K THR 3.1 0.7 + - - -
146K LYS* 3.2 4.7 + - - +
147K ILE* 3.0 36.0 + - + +
160K HEM 4.8 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 144 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113K PHE* 3.6 28.9 - - + +
114K LYS* 5.9 0.4 - - - -
116K PHE* 4.1 13.2 - - + -
117K GLY* 3.5 33.0 - - - +
120K LEU* 5.3 4.9 - - + -
140K LEU* 2.8 36.8 + - + +
141K LYS* 3.9 4.5 - - - +
143K ILE* 1.3 75.4 - - + +
145K THR* 1.3 63.5 + - - +
147K ILE* 3.3 6.2 + - - +
148K SER* 3.1 22.8 + - - -
160K HEM 3.3 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 145 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141K LYS* 2.9 33.9 + - - +
142K GLY* 3.9 5.8 - - - -
144K LEU* 1.3 76.8 - - - +
146K LYS* 1.3 67.5 + - + +
148K SER* 3.0 10.6 + - - +
149K SER* 3.0 25.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 146 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91K LEU* 5.9 4.8 - - - +
92K ASP* 3.9 27.5 + - - +
95K LEU* 4.2 35.0 - - + +
96K ASP* 5.0 5.2 - - + +
99K ALA* 3.8 8.1 - - - +
142K GLY* 3.2 22.5 + - - +
143K ILE 3.2 4.7 + - - +
145K THR* 1.3 81.0 - - + +
147K ILE* 1.3 58.5 + - - +
149K SER* 2.8 25.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 147 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95K LEU* 3.4 23.1 - - + -
98K LEU* 3.9 34.7 - - + +
99K ALA* 3.0 26.7 - - - +
102K HIS* 4.3 13.2 - - + +
113K PHE* 3.4 21.5 - - + -
143K ILE* 3.0 36.2 + - + +
144K LEU* 3.6 7.6 - - - +
145K THR 3.0 0.8 + - - -
146K LYS* 1.3 80.0 - - - +
148K SER* 1.3 58.1 + - - +
149K SER 3.4 0.2 - - - -
150K ARG* 4.8 0.7 + - - +
160K HEM 3.8 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 148 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102K HIS* 5.9 0.4 - - - -
110K LYS* 4.0 20.8 - - - +
113K PHE* 3.8 27.8 - - - +
144K LEU 3.1 17.1 + - - -
145K THR* 3.1 9.0 + - - -
147K ILE* 1.3 75.3 - - - +
149K SER* 1.3 51.8 + - - +
150K ARG 2.5 20.2 + - - -
151K LEU* 3.4 34.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 149 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96K ASP* 5.6 1.6 + - - -
99K ALA* 4.4 5.5 - - - +
110K LYS* 4.8 11.2 - - - +
145K THR* 3.0 16.0 + - - -
146K LYS* 2.8 27.2 + - - +
147K ILE 3.4 1.2 - - - -
148K SER* 1.3 73.7 - - - +
150K ARG* 1.3 65.5 + - - +
151K LEU 4.2 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