Contacts of the helix formed by residues 108 - 127 (chain I) 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 THR 108 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106I GLY 4.0 4.5 - - - +
107I VAL* 1.3 84.4 - - - +
109I LYS* 1.3 63.7 + - - +
110I GLU* 3.1 15.1 + - - +
111I TYR* 2.8 59.1 + - + +
112I PHE* 3.8 9.5 + - - -
150I LEU* 4.1 5.7 - - - +
151I PRO* 4.5 8.1 - - - +
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Residues in contact with LYS 109 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108I THR* 1.3 74.7 - - - +
110I GLU* 1.3 62.9 + - - +
112I PHE* 3.6 6.4 + - - +
113I ARG* 3.5 15.6 + - - +
143I VAL* 5.8 0.3 - - - +
144I ALA* 5.9 1.3 - - - +
147I ALA* 3.6 27.1 - - + +
148I LYS* 4.1 14.5 + - - +
150I LEU* 4.4 4.3 - - - -
151I PRO* 3.5 45.7 - - + +
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Residues in contact with GLU 110 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46I TYR* 3.5 32.0 - - + -
108I THR* 3.2 12.4 + - - +
109I LYS* 1.3 76.3 - - - +
111I TYR* 1.3 73.4 + - - +
112I PHE 3.0 2.0 - - - -
113I ARG* 2.8 35.3 + - - +
114I GLY* 2.8 18.9 + - - -
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Residues in contact with TYR 111 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42I LEU* 3.9 7.4 - - + +
46I TYR* 4.1 21.3 - + + -
48I THR* 3.1 32.6 + - - +
49I SER* 3.5 34.9 + - - -
52I LEU* 4.0 11.8 - - + +
106I GLY 3.2 23.2 + - - -
107I VAL* 4.1 3.4 - - - -
108I THR* 2.8 52.2 + - + +
110I GLU* 1.3 78.5 - - - +
112I PHE* 1.3 56.3 + - - +
114I GLY* 3.1 4.1 + - - +
115I ILE 2.9 22.9 + - - -
160I HEM 3.5 27.7 - - + +
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Residues in contact with PHE 112 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101I HIS* 3.5 16.4 - + - -
107I VAL* 3.8 8.5 - - + -
108I THR 3.8 5.8 + - - -
109I LYS 3.6 9.3 + - - +
110I GLU 2.9 1.2 + - - -
111I TYR* 1.3 74.9 - - - +
113I ARG* 1.3 64.3 + - - +
114I GLY 2.8 5.8 + - - -
115I ILE* 2.9 16.1 + - + +
116I GLY* 3.0 10.6 + - - -
143I VAL* 3.9 36.2 - - + +
146I ILE* 3.4 33.2 - - + -
147I ALA* 4.1 7.9 - - + -
150I LEU* 3.4 27.4 - - + -
160I HEM 3.4 58.8 - + + -
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Residues in contact with ARG 113 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46I TYR* 3.6 17.4 + - - -
109I LYS 3.5 8.0 + - - +
110I GLU* 2.8 38.7 + - - +
112I PHE* 1.3 75.8 - - - +
114I GLY* 1.3 57.8 - - - +
116I GLY* 3.5 3.3 + - - +
117I GLU* 2.9 43.1 + - + +
140I HIS* 5.7 7.4 - - - +
143I VAL* 4.7 7.0 - - + +
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Residues in contact with GLY 114 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41I ASP* 4.9 1.7 - - - +
42I LEU* 3.9 10.6 - - - +
46I TYR* 3.8 30.1 - - - -
110I GLU 2.8 11.2 + - - -
111I TYR 3.4 5.2 - - - -
112I PHE 2.8 2.6 - - - -
113I ARG* 1.3 75.7 - - - +
115I ILE* 1.3 62.5 + - - -
116I GLY 3.0 1.6 - - - -
117I GLU* 3.2 9.3 + - - +
118I ALA* 3.1 18.5 + - - +
121I ARG* 5.2 0.5 + - - -
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Residues in contact with ILE 115 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38I VAL* 4.0 11.4 - - + -
39I PHE* 3.8 32.5 - - + -
42I LEU* 3.9 13.2 - - + +
73I VAL* 5.5 1.8 - - + -
111I TYR 2.9 11.4 + - - +
112I PHE* 2.9 13.2 + - + +
114I GLY* 1.3 73.7 - - - +
116I GLY* 1.3 70.8 + - - +
118I ALA* 3.0 20.5 - - + +
119I PHE* 3.2 31.5 - - + -
139I PHE* 4.6 4.0 - - + -
160I HEM 3.8 52.3 - - + -
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Residues in contact with GLY 116 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112I PHE 3.0 13.1 + - - -
113I ARG* 3.5 4.0 + - - -
114I GLY 3.0 0.2 - - - -
115I ILE* 1.3 77.4 - - - +
117I GLU* 1.3 64.6 + - - +
118I ALA 3.4 0.2 + - - -
119I PHE* 3.5 3.6 + - - +
120I ALA* 3.3 21.0 + - - +
135I TRP* 5.0 0.3 + - - -
136I ASN* 4.5 6.6 + - - -
139I PHE* 3.4 29.0 - - - -
140I HIS* 5.9 6.3 - - - -
143I VAL* 5.5 0.7 - - - -
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Residues in contact with GLU 117 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45I HIS* 5.1 2.3 - - - -
46I TYR* 3.0 37.0 + - - -
113I ARG* 2.9 34.3 + - + +
114I GLY* 3.5 4.2 - - - +
116I GLY* 1.3 74.8 - - - +
118I ALA* 1.3 66.9 + - - +
120I ALA* 3.1 17.4 + - - +
121I ARG* 3.1 41.9 + - - +
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Residues in contact with ALA 118 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38I VAL* 3.5 32.5 - - + +
41I ASP* 3.5 19.7 + - + +
42I LEU 4.6 3.4 - - - +
114I GLY 3.1 7.8 + - - +
115I ILE* 3.0 22.4 - - + +
117I GLU* 1.3 74.2 - - - +
119I PHE* 1.3 64.8 + - - +
121I ARG* 2.8 13.7 + - - +
122I VAL* 2.9 19.2 + - - +
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Residues in contact with PHE 119 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I TRP* 5.2 4.5 - + - -
34I ILE* 5.7 2.2 - - + -
35I VAL* 5.6 11.9 - - + -
38I VAL* 3.7 35.2 - - + +
73I VAL* 6.0 4.0 - - + -
77I LEU* 3.4 30.3 - - + -
115I ILE* 3.2 39.9 + - + -
116I GLY 4.0 3.1 - - - +
118I ALA* 1.3 77.6 - - - +
120I ALA* 1.3 54.9 + - - +
121I ARG 2.8 10.7 + - - -
122I VAL* 2.9 4.9 + - - +
123I LEU* 2.8 52.8 + - + +
124I PRO* 3.4 2.1 - - - +
135I TRP* 3.9 23.6 - + - +
139I PHE* 3.8 21.5 - + - -
160I HEM 4.3 3.1 - - + -
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Residues in contact with ALA 120 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116I GLY 3.3 10.3 + - - +
117I GLU* 3.1 14.5 + - - +
119I PHE* 1.3 76.5 - - - +
121I ARG* 1.3 56.0 + - - +
124I PRO* 3.3 19.0 - - - +
130I PHE* 4.8 8.5 - - - -
132I VAL* 4.5 14.2 - - + +
135I TRP* 4.6 3.3 - - + +
136I ASN* 3.7 28.9 - - - +
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Residues in contact with ARG 121 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41I ASP* 2.7 39.5 + - - +
45I HIS* 3.3 35.8 + - - -
46I TYR* 5.9 0.2 - - - -
114I GLY 5.2 0.8 + - - -
117I GLU* 3.1 37.8 + - - +
118I ALA 2.8 8.4 + - - +
120I ALA* 1.3 77.6 - - - +
122I VAL* 1.3 64.0 + - + +
124I PRO* 3.5 10.8 - - - +
125I GLN* 3.3 20.3 - - - +
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Residues in contact with VAL 122 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34I ILE* 4.4 9.6 - - + +
37I ALA* 3.8 19.3 - - + +
38I VAL* 3.7 36.8 - - + -
41I ASP* 4.6 7.9 - - + +
118I ALA 3.1 17.0 - - - +
119I PHE* 2.9 3.1 + - - +
121I ARG* 1.3 76.0 - - + +
123I LEU* 1.3 55.6 + - + +
124I PRO* 3.2 2.0 - - - -
125I GLN* 2.6 41.8 + - - +
126I VAL* 3.4 4.5 + - + -
7J LEU* 4.1 27.4 - - + -
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Residues in contact with LEU 123 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I ILE* 5.6 1.3 - - + -
19I TRP* 5.0 6.7 - - + -
22I VAL* 4.2 20.0 - - + -
34I ILE* 4.4 14.8 - - + -
119I PHE* 2.8 32.6 + - + +
122I VAL* 1.3 73.6 - - + +
124I PRO* 1.3 59.0 - - + +
125I GLN 2.6 12.6 + - - -
126I VAL* 2.9 27.3 + - + -
127I LEU* 2.9 18.8 + - + +
130I PHE* 3.5 33.9 - - + -
135I TRP* 3.6 36.3 - - + -
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Residues in contact with PRO 124 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119I PHE 3.4 9.2 - - - +
120I ALA 3.3 21.5 - - - +
121I ARG* 3.5 14.1 - - - +
122I VAL 3.2 1.3 - - - -
123I LEU* 1.3 91.8 - - + +
125I GLN* 1.3 58.1 + - + +
127I LEU 3.6 9.5 - - - +
128I SER* 5.5 0.2 - - - -
130I PHE* 3.8 25.7 - - + -
132I VAL* 5.8 2.9 - - + -
11J LYS* 3.5 12.8 + - - -
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Residues in contact with GLN 125 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121I ARG 3.3 20.2 - - - +
122I VAL* 2.6 12.6 + - - +
123I LEU 2.6 5.5 + - - -
124I PRO* 1.3 75.5 - - + +
126I VAL* 1.3 57.3 + - - -
127I LEU 3.4 1.6 - - - -
2J LYS* 5.3 14.8 + - - +
7J LEU* 3.5 37.5 - - + +
8J GLU* 4.1 20.6 + - - +
11J LYS* 2.9 26.2 + - - +
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Residues in contact with VAL 126 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I ARG* 3.8 13.5 + - - +
34I ILE* 3.9 31.4 - - + -
122I VAL* 3.7 3.4 - - + +
123I LEU* 3.1 35.4 - - + +
125I GLN* 1.3 74.6 - - - +
127I LEU* 1.3 73.7 + - + +
7J LEU* 3.2 42.0 - - + -
10J LEU* 4.2 9.1 - - + -
11J LYS* 3.5 22.6 + - - -
14J SER* 5.5 0.2 - - - -
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Residues in contact with LEU 127 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I ILE* 3.7 39.9 - - + +
21I ASP* 3.2 28.5 - - + +
22I VAL* 3.8 18.6 - - + -
30I ARG* 5.3 1.8 - - - +
123I LEU* 2.9 37.4 - - + +
124I PRO* 3.6 19.8 - - - +
125I GLN 3.4 0.8 - - - -
126I VAL* 1.3 93.1 - - + +
128I SER* 1.3 68.4 + - - +
129I CYS 5.3 1.8 - - - +
130I PHE* 4.3 10.3 - - + +
11J LYS* 3.5 11.5 - - - +
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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
------------------------------------------------------------
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