Contacts of the helix formed by residues 102 - 122 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100B LYS 3.0 12.3 - - - +
101B ILE* 1.3 86.9 - - - +
103B ASP* 1.3 56.6 + - - +
104B ASN* 2.7 25.9 + - + +
105B TYR* 2.9 56.8 + - + +
106B PHE* 3.7 5.5 + - - -
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Residues in contact with ASP 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B ILE 4.6 3.8 - - - +
102B PRO* 1.3 71.4 - - - +
104B ASN* 1.3 62.4 + - - +
106B PHE* 3.7 10.4 + - - +
107B ASP* 3.3 21.5 + - - +
142B LYS* 3.6 34.9 + - - +
144B HIS* 3.8 27.9 + - - +
145B HIS* 4.5 3.6 - - - +
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Residues in contact with ASN 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B VAL* 4.2 13.9 - - - +
43B GLU* 6.3 0.4 - - - +
102B PRO* 2.7 15.4 + - + +
103B ASP* 1.3 79.5 - - - +
105B TYR* 1.3 88.6 + - - +
107B ASP* 3.2 19.0 - - - +
108B ALA* 3.4 6.9 + - - +
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Residues in contact with TYR 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B THR* 5.5 1.5 - - + +
41B VAL* 4.0 20.6 - - + -
43B GLU* 3.3 27.7 + - + +
44B SER* 3.3 28.4 + - - -
46B SER* 5.2 0.2 + - - -
47B LEU* 3.9 20.7 - - + +
100B LYS 5.2 0.2 - - - -
101B ILE* 4.1 1.3 - - + -
102B PRO* 2.9 32.9 + - + +
104B ASN* 1.3 93.5 - - - +
106B PHE* 1.3 67.8 + - - +
107B ASP 3.0 1.8 - - - -
108B ALA* 2.8 18.9 + - - +
109B PHE* 2.9 11.8 + - - +
160B HEM 3.6 40.2 - - + -
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Residues in contact with PHE 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B HIS* 4.8 3.6 - + + -
101B ILE* 3.3 43.1 - - + -
102B PRO 3.9 8.1 - - - -
103B ASP* 3.7 7.8 + - - +
104B ASN 3.5 0.4 - - - -
105B TYR* 1.3 78.0 - - - +
107B ASP* 1.3 63.0 + - - +
109B PHE* 3.3 1.1 + - - +
110B LYS* 2.9 12.1 + - - +
138B GLU* 2.8 51.7 - - + +
141B ILE* 4.3 25.1 - - + -
142B LYS* 3.9 40.8 - - + +
160B HEM 3.6 39.4 - + + +
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Residues in contact with ASP 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ASP 3.3 11.5 + - - +
104B ASN* 3.2 13.9 - - - +
105B TYR 2.9 0.6 + - - -
106B PHE* 1.3 78.0 - - - +
108B ALA* 1.3 64.1 + - - +
110B LYS* 3.2 25.2 + - - +
111B THR* 3.0 28.5 + - - -
138B GLU* 4.6 2.0 + - - -
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Residues in contact with ALA 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B THR* 4.4 4.9 - - + +
40B GLN* 2.9 46.1 - - + +
41B VAL* 4.0 25.6 - - + -
104B ASN 3.4 3.9 + - - +
105B TYR 2.8 13.5 + - - +
107B ASP* 1.3 75.8 - - - +
109B PHE* 1.3 50.9 + - - +
111B THR* 3.1 2.0 + - - -
112B ALA* 2.7 32.7 + - - +
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Residues in contact with PHE 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ILE* 4.2 13.0 - - + -
34B TRP* 3.4 41.3 - + - -
37B THR* 3.3 25.5 + - + +
68B VAL* 4.2 20.2 - - + -
69B LEU* 5.4 5.6 - - + -
72B LEU* 5.1 4.0 - - + -
105B TYR 2.9 11.0 + - - +
106B PHE* 3.6 8.1 - - - +
108B ALA* 1.3 76.6 - - - +
110B LYS* 1.3 63.1 + - - +
112B ALA* 3.4 1.4 - - - +
113B ILE* 3.0 52.8 + - + +
138B GLU* 4.3 4.3 - - - -
160B HEM 3.6 45.8 - + + -
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Residues in contact with LYS 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B PHE 2.9 13.0 + - - +
107B ASP* 3.4 26.0 + - - +
109B PHE* 1.3 73.7 - - - +
111B THR* 1.3 74.4 + - - +
113B ILE* 3.0 7.3 + - - +
114B LEU* 2.8 34.1 + - + +
131B ASP* 3.5 33.0 + - - +
134B ILE* 3.2 33.0 - - + -
135B ASP* 3.0 28.2 + - - +
138B GLU* 3.7 14.1 + - - +
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Residues in contact with THR 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B GLN* 3.7 23.3 + - - +
107B ASP* 3.0 17.5 + - - -
108B ALA 3.3 7.9 - - - -
110B LYS* 1.3 84.3 - - - +
112B ALA* 1.3 67.6 + - - +
114B LEU* 3.1 7.6 + - - +
115B HIS* 2.8 50.7 + - + +
127B ARG* 6.3 0.9 - - - +
140M PHE* 3.7 10.8 - - + -
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Residues in contact with ALA 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ILE* 3.4 20.2 - - + +
36B ALA* 3.8 11.4 - - + -
37B THR* 3.2 35.9 - - - +
40B GLN* 3.9 2.2 + - - +
108B ALA 2.7 13.7 + - - +
109B PHE 3.4 5.6 - - - +
111B THR* 1.3 75.9 - - - +
113B ILE* 1.3 65.7 + - - +
115B HIS* 3.0 3.6 + - - +
116B VAL* 2.9 25.4 + - - +
140M PHE* 5.3 0.9 - - - -
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Residues in contact with ILE 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B TRP* 5.0 1.6 - - + -
33B ILE* 4.0 27.8 - - + +
69B LEU* 5.8 0.2 - - + -
72B LEU* 3.6 26.5 - - + -
109B PHE* 3.0 45.5 + - + +
110B LYS* 3.0 10.3 + - - +
112B ALA* 1.3 78.8 - - - +
114B LEU* 1.3 69.3 + - + +
116B VAL* 3.2 0.9 + - - +
117B VAL* 2.8 49.7 + - + +
130B TRP* 4.3 10.8 - - + -
134B ILE* 4.2 16.4 - - + -
160B HEM 5.6 1.1 - - + -
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Residues in contact with LEU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B LYS* 2.8 32.2 + - + +
111B THR* 3.5 10.1 - - - +
113B ILE* 1.3 77.9 - - + +
115B HIS* 1.3 66.9 + - + +
117B VAL* 3.4 3.7 + - - +
118B ALA* 2.9 26.1 + - - +
125B TYR* 3.5 21.9 + - - +
127B ARG* 4.5 22.0 - - + +
130B TRP* 4.1 16.8 - - + -
131B ASP* 4.1 33.0 - - + +
134B ILE* 4.0 27.1 - - + -
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Residues in contact with HIS 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B ALA* 5.9 0.4 - - + -
111B THR* 2.8 40.1 + - + +
112B ALA* 3.6 6.7 - - - +
114B LEU* 1.3 75.2 - - + +
116B VAL* 1.3 63.0 + - + +
118B ALA* 3.4 5.6 + - - +
119B ALA* 3.0 17.5 + - - +
127B ARG* 5.5 10.8 - - - -
138M LYS* 3.6 34.0 + - + +
140M PHE* 3.6 28.7 - + + -
141M PHE* 3.1 33.5 - + + -
146M TRP* 3.9 17.4 - + - -
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Residues in contact with VAL 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B PHE* 3.6 22.4 - - + +
32B ALA* 3.9 3.6 - - + +
33B ILE* 3.6 36.8 - - + +
36B ALA* 4.7 2.7 - - + -
112B ALA 2.9 15.8 + - - +
113B ILE 3.7 4.5 - - - +
115B HIS* 1.3 75.1 - - - +
117B VAL* 1.3 65.1 + - - +
119B ALA* 2.8 5.7 + - - +
120B GLN* 2.8 19.8 + - - +
80M LEU* 3.6 28.9 - - + -
141M PHE* 3.7 25.1 - - + -
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Residues in contact with VAL 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ALA* 4.0 4.5 - - + -
29B PHE* 3.7 30.1 - - + -
113B ILE* 2.8 30.4 + - + +
114B LEU* 3.7 4.3 - - - +
116B VAL* 1.3 72.4 - - - +
118B ALA* 1.3 58.0 + - - +
120B GLN* 3.0 3.4 + - - -
121B LEU* 2.8 52.5 + - + +
125B TYR* 3.6 16.8 - - + -
130B TRP* 3.7 35.4 - - + -
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Residues in contact with ALA 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B LEU 2.9 18.8 + - - +
115B HIS* 3.6 6.1 - - - +
117B VAL* 1.3 75.8 - - - +
119B ALA* 1.3 63.1 + - - +
121B LEU* 4.1 0.7 - - - +
122B GLY* 3.3 25.3 + - - +
125B TYR* 3.8 33.1 - - + +
146M TRP* 3.8 17.3 - - + -
170M PHE* 4.0 2.9 - - - -
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Residues in contact with ALA 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B HIS 3.0 4.8 + - - +
116B VAL 2.8 9.7 + - - +
118B ALA* 1.3 77.7 - - - +
120B GLN* 1.3 61.0 + - - +
122B GLY 3.8 0.9 + - - -
80M LEU* 4.3 4.3 - - + -
141M PHE* 3.5 32.3 - - + -
144M ARG* 2.8 50.2 + - + +
146M TRP* 3.6 6.9 - - + -
170M PHE* 3.8 7.7 - - - -
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Residues in contact with GLN 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ARG 4.8 1.7 - - - +
19B ALA* 3.3 28.9 - - + +
25B ASP* 4.7 6.9 - - - +
29B PHE* 4.0 12.0 - - + +
116B VAL 2.8 9.5 + - - +
117B VAL* 3.0 10.5 + - - +
119B ALA* 1.3 78.4 - - - +
121B LEU* 1.3 62.7 + - - +
122B GLY 3.5 0.3 + - - -
65M HIS* 3.6 33.5 + - - -
78M HIS* 3.1 35.2 + - - -
79M ASP* 5.7 0.6 - - - +
80M LEU* 3.5 31.3 - - + +
144M ARG* 5.0 1.4 - - - +
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Residues in contact with LEU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B GLU* 3.8 24.2 - - + +
18B ARG* 3.6 29.2 + - + +
19B ALA* 3.6 31.2 - - + +
117B VAL* 2.8 39.7 + - + +
118B ALA 4.5 0.9 - - - +
120B GLN* 1.3 75.6 - - - +
122B GLY* 1.3 59.7 + - - +
123B ARG* 2.8 26.3 + - - -
124B CYS 3.8 23.1 + - - +
125B TYR* 3.8 15.9 - - + -
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Residues in contact with GLY 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B ALA 3.3 12.3 + - - +
119B ALA 3.8 1.2 + - - -
120B GLN 3.3 4.4 + - - -
121B LEU* 1.3 74.9 - - - +
123B ARG* 1.3 63.1 + - - -
125B TYR* 5.7 1.5 - - - +
146M TRP* 5.9 0.9 - - - -
170M PHE* 3.5 36.0 - - - -
179M LEU* 4.6 7.9 - - - -
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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