Contacts of the helix formed by residues 98 - 111 (chain B) in PDB entry 2GB0
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 SER 98 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94B PRO* 3.7 14.7 + - - -
96B GLY* 3.7 2.4 - - - +
97B GLU* 1.3 79.9 - - - +
99B ALA* 1.3 58.4 + - - +
101B VAL* 2.9 37.7 + - - +
102B ALA* 3.0 27.1 + - - +
247B GLU* 2.5 34.2 + - - +
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Residues in contact with ALA 99 (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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96A GLY 3.5 24.7 - - - +
97A GLU* 3.9 27.1 + - + +
56B GLY 5.4 0.2 - - - -
97B GLU 4.2 0.8 - - - -
98B SER* 1.3 72.1 + - - +
100B PHE* 1.3 58.9 + - - +
102B ALA* 3.6 6.1 - - - +
103B GLU* 2.8 33.7 + - - +
247B GLU* 3.9 3.0 + - - +
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Residues in contact with PHE 100 (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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52B ARG* 3.5 34.3 - - - -
56B GLY* 3.6 24.4 - - - -
57B GLU* 3.8 7.2 - - + -
91B VAL* 3.6 15.5 - - + -
99B ALA* 1.3 80.7 - - - +
101B VAL* 1.3 65.7 + - + +
103B GLU 3.4 0.2 + - - -
104B THR* 2.8 29.0 + - - -
245B MET* 3.5 64.6 - - + -
246B VAL 5.0 0.2 - - - -
247B GLU* 3.5 24.7 + - + +
252B ILE* 4.3 18.6 - - + -
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Residues in contact with VAL 101 (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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91B VAL* 3.9 22.0 - - + +
92B PHE 3.5 33.2 - - - +
93B GLY* 3.7 3.8 - - - +
94B PRO 5.9 0.2 - - - +
98B SER* 2.9 28.1 + - - +
100B PHE* 1.3 79.0 - - + +
102B ALA* 1.3 64.3 + - - +
104B THR* 3.3 2.4 + - - -
105B MET* 3.0 50.7 + - + +
137B ASN* 3.9 17.7 - - - +
139B ILE* 4.7 2.0 - - + -
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Residues in contact with ALA 102 (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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98B SER 3.0 18.8 + - - +
99B ALA* 3.6 7.6 - - - +
101B VAL* 1.3 79.8 - - - +
103B GLU* 1.3 58.1 + - - +
105B MET* 3.4 9.2 + - - +
106B GLU* 3.0 30.6 + - + +
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Residues in contact with GLU 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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55B TYR 3.6 9.6 - - - +
56B GLY 3.3 25.6 - - - +
57B GLU 4.7 0.7 - - - -
58B GLY* 3.6 8.0 - - - +
59B ARG* 2.8 63.2 + - - +
60B GLU* 4.7 0.3 - - - +
99B ALA 2.8 19.3 + - - +
102B ALA* 1.3 71.5 - - - +
104B THR* 1.3 60.8 + - - +
106B GLU* 4.3 1.7 - - - +
107B ALA* 2.8 28.6 + - - +
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Residues in contact with THR 104 (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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52B ARG* 3.3 20.9 + - - +
54B ALA* 3.6 16.3 - - + +
55B TYR 4.4 2.0 - - - -
56B GLY* 3.1 20.6 - - - +
91B VAL* 4.0 14.1 - - + +
100B PHE* 2.8 24.8 + - - -
101B VAL 3.5 5.2 - - - -
103B GLU* 1.3 76.1 - - - +
105B MET* 1.3 62.9 + - - +
107B ALA* 3.2 3.5 + - - +
108B ALA* 3.0 22.7 + - - +
139B ILE* 3.6 26.2 - - + -
141B GLU* 5.1 3.1 - - + +
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Residues in contact with MET 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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101B VAL* 3.0 36.3 + - + +
102B ALA* 3.6 7.9 - - - +
104B THR* 1.3 76.7 - - - +
106B GLU* 1.3 62.2 + - + +
108B ALA* 3.4 3.1 + - - +
109B LYS* 3.1 24.1 + - - +
117B LEU* 4.2 15.9 - - + -
137B ASN* 3.6 30.3 - - + +
138B ALA 3.7 26.0 - - - +
139B ILE* 3.7 23.1 - - + -
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Residues in contact with GLU 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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59B ARG* 3.5 38.3 + - - +
102B ALA* 3.0 19.1 + - + +
103B GLU* 3.2 6.0 + - - +
105B MET* 1.3 72.8 - - - +
107B ALA* 1.3 61.1 + - - +
109B LYS* 3.3 25.8 + - - +
110B GLU* 2.8 34.2 + - - +
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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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54B ALA* 4.1 2.0 - - - -
55B TYR 3.6 28.5 - - - +
59B ARG* 3.8 29.5 - - + +
62B VAL* 4.4 4.0 - - + -
103B GLU 2.8 17.7 + - - +
104B THR 3.6 4.3 - - - +
106B GLU* 1.3 77.4 - - - +
108B ALA* 1.3 61.6 + - - +
110B GLU* 3.3 0.8 + - - -
111B HIS* 3.0 31.6 + - - +
113B LEU* 4.5 1.5 - - - +
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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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54B ALA* 4.0 6.4 - - + +
104B THR 3.0 15.5 + - - +
105B MET 3.7 4.9 - - - +
106B GLU 3.3 0.2 - - - -
107B ALA* 1.3 78.5 - - - +
109B LYS* 1.3 56.8 + - - +
112B SER* 3.0 9.2 + - - -
113B LEU* 2.9 41.4 + - + +
115B VAL* 3.9 24.5 - - + -
139B ILE* 3.7 20.0 - - + -
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Residues in contact with LYS 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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105B MET 3.1 17.5 + - - +
106B GLU* 3.6 25.6 + - - +
108B ALA* 1.3 76.5 - - - +
110B GLU* 1.3 62.8 + - - +
112B SER* 3.2 15.9 + - - +
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Residues in contact with GLU 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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59B ARG* 2.7 53.6 + - - +
106B GLU* 2.8 19.5 + - - +
107B ALA* 3.7 4.9 - - - +
109B LYS* 1.3 78.8 - - - +
111B HIS* 1.3 73.4 + - + +
112B SER* 3.4 2.0 + - - -
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Residues in contact with HIS 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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59B ARG* 3.5 29.2 + - + -
62B VAL* 3.6 30.7 - - + +
63B PRO* 4.6 10.2 - - + +
66B LEU* 5.6 2.9 - - + -
107B ALA 3.0 26.4 + - - +
110B GLU* 1.3 104.8 + - + +
112B SER* 1.3 70.8 + - - +
113B LEU* 3.2 21.0 + - + +
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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
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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