Contacts of the helix formed by residues 93 - 108 (chain B) in PDB entry 2G33
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 VAL 93 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ASP* 6.0 4.7 - - + +
62B TRP* 4.1 20.9 - - + -
65B LEU* 4.8 8.7 - - + -
88B TYR* 3.1 26.4 + - + +
89B VAL* 2.9 20.8 + - + +
92B ASN* 1.3 83.2 - - - +
94B GLY* 1.3 69.1 + - - +
95B LEU 2.6 7.1 + - - -
96B LYS* 2.8 16.1 + - + +
97B PHE* 2.7 35.3 + - + +
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Residues in contact with GLY 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B VAL* 4.3 16.8 - - - -
62B TRP* 4.6 7.6 - - - -
89B VAL 2.8 16.9 + - - -
90B ASN* 4.4 11.7 - - - -
91B THR 3.8 1.6 + - - -
93B VAL* 1.3 73.9 - - - +
95B LEU* 1.3 51.2 + - - +
97B PHE* 3.9 4.2 - - - +
98B ARG* 2.5 47.7 + - - +
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Residues in contact with LEU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU 5.6 3.1 - - - +
21B SER* 3.8 33.4 - - - +
24B PHE* 5.7 8.5 - - + -
91B THR 3.6 19.0 + - - +
92B ASN* 4.5 5.6 - - - +
93B VAL 2.6 0.8 + - - -
94B GLY* 1.3 72.0 - - - +
96B LYS* 1.3 79.8 + - + +
97B PHE 2.5 17.1 + - - -
98B ARG* 2.8 9.0 + - - +
99B GLN* 2.7 43.7 + - + +
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Residues in contact with LYS 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ASP* 3.5 34.8 + - - +
67A THR* 4.0 21.6 - - - +
6B TYR* 5.3 0.2 + - - -
88B TYR* 5.2 4.6 + - - -
92B ASN 4.2 15.3 - - - +
93B VAL* 2.8 21.1 + - + +
95B LEU* 1.3 88.1 - - + +
97B PHE* 1.3 68.5 + - + +
99B GLN* 4.0 13.0 - - - +
100B LEU* 3.5 20.4 + - - +
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Residues in contact with PHE 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ALA* 4.9 12.3 - - + -
64A ASP* 4.4 16.2 - - + -
27B VAL* 5.7 4.7 - - + -
58B ALA* 3.4 19.5 - - + -
61B ALA* 4.5 9.6 - - + -
62B TRP* 3.1 63.7 - + + -
65B LEU* 4.6 9.4 - - + -
93B VAL* 2.7 26.4 + - + +
94B GLY 3.9 3.1 - - - +
95B LEU 2.5 6.5 + - - -
96B LYS* 1.3 79.7 - - + +
98B ARG* 1.3 59.9 + - - +
99B GLN 3.3 0.4 - - - -
100B LEU* 3.5 11.6 - - + +
101B LEU* 2.9 42.8 + - + +
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Residues in contact with ARG 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B SER* 3.2 26.7 + - - +
24B PHE* 3.4 36.9 + - + +
25B PRO 2.8 23.9 + - - +
26B SER* 3.5 21.6 - - - +
27B VAL* 3.4 34.9 - - + +
30B LEU* 4.2 5.8 - - + -
94B GLY* 2.5 32.0 + - - +
95B LEU* 2.8 6.0 + - - +
97B PHE* 1.3 69.0 - - - +
99B GLN* 1.3 72.3 - - - +
100B LEU 3.1 0.3 + - - -
101B LEU* 3.2 7.5 + - - -
102B TRP* 3.1 24.3 + - - +
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Residues in contact with GLN 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B TYR* 4.1 10.0 + - - +
13B VAL* 4.4 17.4 - - - +
16B LEU* 3.5 50.8 + - + +
17B SER* 4.6 2.2 - - - +
19B LEU* 5.4 0.8 - - - +
24B PHE* 3.6 25.0 - - + -
95B LEU* 2.7 36.7 + - + +
96B LYS* 4.0 15.3 - - - +
98B ARG* 1.3 75.4 - - - +
100B LEU* 1.3 66.4 + - - +
102B TRP* 3.8 10.9 - - - -
103B PHE* 3.6 9.2 + - - +
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Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLN* 4.9 10.5 - - - +
5B PRO* 6.3 3.6 - - + -
6B TYR* 3.4 23.1 - - + +
55B LEU* 5.8 1.3 - - + -
58B ALA* 4.3 27.8 - - + -
96B LYS 3.5 13.9 + - - +
97B PHE* 3.5 19.0 + - + +
99B GLN* 1.3 86.1 - - - +
101B LEU* 1.3 93.3 + - + +
103B PHE* 2.6 20.4 - - - +
104B HIS* 3.5 27.4 - - + +
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Residues in contact with LEU 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B VAL* 5.2 6.3 - - + +
30B LEU* 3.6 25.1 - - + +
31B LEU* 4.4 20.4 - - + -
55B LEU* 5.4 6.3 - - + -
58B ALA* 4.4 16.4 - - + -
59B ILE* 5.1 12.8 - - + +
62B TRP* 6.2 0.9 - - + -
97B PHE* 2.9 33.5 + - + +
98B ARG* 3.5 4.3 - - - +
100B LEU* 1.3 90.6 - - + +
102B TRP* 1.3 66.4 + - - +
103B PHE 2.6 2.4 + - - -
104B HIS* 2.8 15.3 + - - +
105B ILE* 3.1 36.8 + - + +
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Residues in contact with TRP 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 5.3 11.0 - - + -
19B LEU* 4.3 18.2 - - + -
23B PHE* 4.0 30.4 - + - -
24B PHE* 4.0 19.3 - + + -
25B PRO* 5.1 11.0 - - + -
30B LEU* 3.3 18.4 - - + +
98B ARG 3.1 12.7 + - - +
99B GLN 3.8 9.4 - - - -
100B LEU 3.1 1.0 + - - -
101B LEU* 1.3 76.1 - - - +
103B PHE* 1.3 100.8 + + + +
105B ILE* 4.1 6.3 - - - -
106B SER* 2.9 47.8 + - - -
115B VAL* 5.3 6.3 - - + -
118B TYR* 5.3 10.1 - + - -
119B LEU* 4.7 22.2 - - + -
140B LEU* 4.3 18.0 - - + +
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Residues in contact with PHE 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B TYR* 4.1 32.8 - + + -
9B PHE* 4.2 26.7 - + + -
11B ALA* 4.8 10.3 - - + -
16B LEU* 5.1 7.4 - - + -
51B HIS* 4.2 8.3 - + - -
99B GLN 3.9 1.8 - - - +
100B LEU* 2.6 20.9 + - - +
101B LEU 2.6 2.8 + - - -
102B TRP* 1.3 109.3 - + + +
104B HIS* 1.3 117.0 + + - +
106B SER* 4.1 0.3 - - - -
107B ALA* 2.8 23.8 + - + +
112B ARG* 6.3 0.7 - - + -
115B VAL* 5.4 8.0 - - + +
116B LEU* 5.1 11.7 - - + -
119B LEU* 5.6 7.6 - - + -
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Residues in contact with HIS 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLN* 5.3 4.2 + - - -
5B PRO 5.4 2.0 + - - -
6B TYR* 5.5 1.8 - - - -
9B PHE* 3.7 22.8 - + - -
51B HIS* 3.0 36.6 + - + +
54B ALA* 3.9 17.9 - - + +
55B LEU* 4.2 25.3 + - + -
100B LEU* 3.5 31.0 - - + +
101B LEU 2.8 7.4 + - - +
103B PHE* 1.3 111.6 - + - +
105B ILE* 1.3 55.3 + - - +
107B ALA* 2.8 6.0 + - - +
108B LEU* 2.5 40.2 + - + +
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Residues in contact with ILE 105 (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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30B LEU* 3.7 31.4 - - + +
33B THR* 4.7 18.2 - - + -
34B ALA* 4.1 14.6 - - + -
37B LEU* 6.0 2.5 - - + -
38B TYR* 4.0 12.1 + - + -
55B LEU* 4.3 18.5 - - + +
101B LEU* 3.1 39.9 + - + +
102B TRP* 3.6 7.0 - - - +
104B HIS* 1.3 79.3 - - - +
106B SER* 1.3 73.2 + - - +
108B LEU* 3.0 12.9 + - - +
109B THR* 2.9 14.6 + - - +
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Residues in contact with SER 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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102B TRP* 2.9 37.6 + - - -
103B PHE 4.1 0.2 - - - -
105B ILE* 1.3 85.0 - - - +
107B ALA* 1.3 54.1 + - - +
109B THR* 2.8 17.7 + - - -
110B PHE* 2.6 32.2 - - - -
115B VAL* 5.1 0.2 - - - -
140B LEU* 3.7 25.9 - - - +
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Residues in contact with ALA 107 (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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51B HIS* 5.0 15.0 - - + +
103B PHE* 2.8 21.4 + - + +
104B HIS* 2.8 15.7 + - - +
106B SER* 1.3 71.5 - - - +
108B LEU* 1.3 49.8 + - - -
109B THR 2.5 17.6 + - - -
110B PHE 3.0 3.8 + - - -
111B GLY* 2.8 27.0 + - - +
112B ARG* 5.2 1.8 - - - -
115B VAL* 3.6 32.2 - - + +
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Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B TYR* 2.7 50.0 + - + +
42B LEU* 6.1 0.9 - - + -
49B SER* 3.8 9.9 - - - +
51B HIS* 3.0 43.5 - - + -
52B HIS* 3.6 34.5 - - + +
55B LEU* 6.5 2.2 - - + -
104B HIS* 2.5 17.0 + - + +
105B ILE* 3.0 12.9 + - - +
107B ALA* 1.3 69.0 - - - +
109B THR* 1.3 54.7 + - - +
111B GLY 5.1 0.4 - - - -
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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) + - + + + + + -
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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