Contacts of the helix formed by residues 109 - 128 (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 GLN 109 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49K GLU* 3.4 31.8 + - - +
107K GLY 4.1 5.1 - - - +
108K VAL* 1.3 74.8 - - - +
110K LYS* 1.3 66.9 + - - +
111K ALA* 4.2 18.7 - - - +
112K HIS* 2.9 40.1 + - + +
113K PHE* 4.0 3.6 + - - -
151K LEU* 3.7 9.0 - - - -
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Residues in contact with LYS 110 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109K GLN* 1.3 72.2 - - - +
111K ALA* 1.3 53.1 - - - +
112K HIS 2.6 13.2 + - - -
113K PHE* 2.7 18.4 + - - +
114K LYS* 3.2 9.3 + - - +
148K SER* 4.0 30.1 - - - +
149K SER* 4.8 7.3 - - - +
151K LEU* 3.5 25.8 - - + +
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Residues in contact with ALA 111 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47K ILE* 4.4 9.0 - - + +
109K GLN* 3.3 20.7 + - - +
110K LYS* 1.3 76.6 - - - +
112K HIS* 1.3 62.6 + - + +
113K PHE 3.4 0.2 - - - -
114K LYS* 3.6 14.3 + - + +
115K LYS* 3.2 22.2 + - - +
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Residues in contact with HIS 112 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43K LEU* 4.1 6.1 - - + +
47K ILE* 3.8 24.0 - - + -
49K GLU* 3.5 29.3 - - - +
50K VAL* 3.7 10.0 - - + +
53K LEU* 3.6 17.0 - - + -
107K GLY 3.3 24.9 - - - -
108K VAL* 3.7 0.2 - - - -
109K GLN* 2.9 35.2 + - + +
110K LYS 2.6 5.3 + - - -
111K ALA* 1.3 72.2 - - + +
113K PHE* 1.3 62.4 + - + +
115K LYS* 3.2 8.2 + - - +
116K PHE* 2.8 26.7 + - - +
160K HEM 3.4 30.8 - - + +
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Residues in contact with PHE 113 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102K HIS* 3.7 17.5 - + + -
108K VAL* 3.8 21.8 - - + -
109K GLN 4.2 9.4 - - - -
110K LYS 2.7 12.3 + - - +
112K HIS* 1.3 73.2 - - + +
114K LYS* 1.3 68.1 + - - +
116K PHE* 2.9 3.0 + - - +
117K GLY* 2.7 23.0 + - - -
144K LEU* 3.6 41.4 - - + +
147K ILE* 3.4 29.8 - - + -
148K SER* 3.8 26.2 - - - +
151K LEU* 4.7 0.7 - - + -
160K HEM 3.3 48.5 - + + -
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Residues in contact with LYS 114 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110K LYS 3.2 6.5 + - - +
111K ALA* 3.7 16.2 - - - +
113K PHE* 1.3 79.7 - - - +
115K LYS* 1.3 63.2 + - - +
117K GLY* 3.3 2.0 + - - -
118K GLU* 3.2 39.6 + - + +
144K LEU* 5.9 0.9 - - - -
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Residues in contact with LYS 115 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43K LEU* 4.1 9.2 - - + -
46K ASP* 3.0 37.0 - - + +
47K ILE* 4.1 21.1 - - + -
111K ALA 3.2 9.9 + - - +
112K HIS 3.2 9.1 + - - +
113K PHE 3.0 0.6 - - - -
114K LYS* 1.3 76.3 - - - +
116K PHE* 1.3 67.5 + - - +
117K GLY 3.0 1.6 - - - -
118K GLU* 2.9 41.4 + - + +
119K ILE* 2.9 30.3 + - + +
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Residues in contact with PHE 116 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39K LEU* 4.1 39.0 - - + -
40K LEU* 4.0 21.1 - - + -
43K LEU* 4.1 21.0 - - + +
74K ILE* 4.0 18.6 - - + -
78K LEU* 5.8 2.5 - - + -
112K HIS 2.8 17.2 + - - +
113K PHE 3.5 6.5 - - - +
115K LYS* 1.3 73.0 - - - +
117K GLY* 1.3 57.7 + - - +
119K ILE* 3.3 11.8 + - + +
120K LEU* 2.8 50.2 + - + +
144K LEU* 4.1 16.2 - - + -
160K HEM 3.6 39.9 - - + -
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Residues in contact with GLY 117 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113K PHE 2.7 12.3 + - - -
114K LYS 3.6 2.9 - - - -
116K PHE* 1.3 75.2 - - - +
118K GLU* 1.3 64.5 + - - +
120K LEU* 3.1 6.9 + - - +
121K ALA* 2.9 25.3 + - - +
140K LEU* 5.1 3.0 - - - +
144K LEU* 3.5 27.1 - - - -
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Residues in contact with GLU 118 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114K LYS* 3.2 37.8 + - + +
115K LYS* 2.9 33.4 + - + +
117K GLY* 1.3 75.1 - - - +
119K ILE* 1.3 61.2 + - - +
121K ALA* 3.4 7.4 + - - +
122K THR* 2.9 28.5 + - - -
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Residues in contact with ILE 119 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38K LEU* 5.5 1.3 - - + -
39K LEU* 4.1 21.0 - - + +
42K LYS* 3.6 49.6 - - + +
43K LEU* 3.6 33.2 - - + +
46K ASP* 4.9 2.5 - - + +
115K LYS* 2.9 32.9 + - + +
116K PHE* 3.5 10.5 - - + +
118K GLU* 1.3 74.5 - - + +
120K LEU* 1.3 59.4 + - - +
122K THR* 3.0 8.3 + - - -
123K GLY* 2.9 26.7 + - - -
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Residues in contact with LEU 120 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35K PHE* 4.4 0.7 - - + -
39K LEU* 3.4 37.7 - - + +
78K LEU* 4.1 22.0 - - + -
116K PHE* 2.8 37.8 + - + +
117K GLY* 3.5 5.4 - - - +
119K ILE* 1.3 77.0 - - - +
121K ALA* 1.3 56.9 + - - +
124K LEU* 3.0 55.7 + - + +
140K LEU* 3.8 35.9 - - + -
144K LEU* 5.3 7.4 - - + -
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Residues in contact with ALA 121 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117K GLY 2.9 16.7 + - - +
118K GLU* 3.6 8.7 - - - +
119K ILE 3.1 0.2 - - - -
120K LEU* 1.3 78.4 - - - +
122K THR* 1.3 58.5 + - - +
124K LEU* 5.0 0.2 - - - -
125K PRO* 3.1 21.0 - - - +
131K TYR* 3.7 21.6 + - - +
137K LYS* 6.1 7.9 - - + -
140K LEU* 5.0 8.3 - - + -
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Residues in contact with THR 122 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118K GLU 2.9 14.3 + - - -
119K ILE* 3.0 9.2 + - - -
121K ALA* 1.3 79.6 - - - +
123K GLY* 1.3 61.9 + - - +
125K PRO* 3.5 8.2 - - - +
126K GLN* 3.4 26.2 - - - +
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Residues in contact with GLY 123 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35K PHE* 4.3 14.4 - - - -
38K LEU* 6.1 3.1 - - - -
39K LEU* 5.1 4.0 - - - -
119K ILE 2.9 13.7 + - - -
120K LEU* 3.3 2.0 + - - -
122K THR* 1.3 79.7 - - - +
124K LEU* 1.3 67.3 + - - +
125K PRO 3.3 0.2 - - - -
126K GLN* 2.7 31.7 + - - +
127K VAL* 3.7 5.0 + - - +
12L THR* 5.8 0.9 - - - -
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Residues in contact with LEU 124 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19K TRP* 3.9 28.0 - - + -
22K LEU* 5.5 0.2 - - + -
35K PHE* 3.8 24.8 - - + -
78K LEU* 5.7 0.4 - - + -
120K LEU* 3.0 25.4 + - + +
123K GLY* 1.3 70.1 - - - +
125K PRO* 1.3 62.0 - - + +
126K GLN 2.7 11.8 + - - -
127K VAL* 2.8 20.5 + - + +
128K LEU* 3.0 22.6 + - + +
131K TYR* 3.7 14.6 - - + +
136K TRP* 3.3 39.7 - - + -
140K LEU* 4.0 12.6 - - + -
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Residues in contact with PRO 125 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88E LEU* 4.3 20.8 - - + +
121K ALA 3.1 26.5 - - - +
122K THR* 3.5 13.5 - - - +
123K GLY 3.3 0.7 - - - -
124K LEU* 1.3 92.7 - - + +
126K GLN* 1.3 58.5 + - + -
127K VAL 3.4 0.2 - - - -
128K LEU 3.5 19.0 - - - +
131K TYR* 3.6 34.5 - - + -
16L LYS* 3.6 9.4 + - - -
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Residues in contact with GLN 126 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38K LEU* 5.6 1.6 - - - +
122K THR* 3.4 30.1 - - - +
123K GLY* 2.7 16.3 + - - +
124K LEU 2.7 3.4 + - - -
125K PRO* 1.3 74.4 - - + +
127K VAL* 1.3 60.7 + - - +
10L LEU* 5.1 4.8 - - - +
12L THR* 2.6 47.4 + - - +
13L GLU* 5.2 5.5 - - + +
16L LYS* 3.0 32.4 + - - +
131L ASP* 4.4 3.8 - - - +
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Residues in contact with VAL 127 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21K ILE* 5.7 0.2 - - - +
22K LEU* 4.0 15.5 - - + -
35K PHE* 3.9 27.1 - - + -
123K GLY 4.3 1.3 - - - +
124K LEU* 2.8 17.7 + - + +
126K GLN* 1.3 82.7 - - - +
128K LEU* 1.3 79.1 + - + +
129K ASP* 4.0 1.4 + - - +
12L THR* 4.0 18.6 - - - -
15L LEU* 3.9 27.6 - - + -
16L LYS* 3.7 15.3 - - - +
19L LEU* 3.7 22.7 - - - +
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Residues in contact with LEU 128 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18K GLN* 3.7 27.1 - - + +
19K TRP* 4.8 2.2 - - + -
21K ILE* 4.4 12.1 - - + -
22K LEU* 3.5 33.7 - - + -
124K LEU* 3.0 31.1 + - + +
125K PRO* 3.5 19.6 - - - +
127K VAL* 1.3 88.1 - - + +
129K ASP* 1.3 65.7 + - - +
130K ASP 3.4 12.5 + - - +
131K TYR* 4.2 11.3 - - + +
136K TRP* 4.2 22.4 - - + -
16L LYS* 4.0 2.2 - - - -
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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
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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) + - + + + + + -
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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