Contacts of the helix formed by residues 101 - 112 (chain B) in PDB entry 2G9Y
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 ASP 101 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100B THR* 1.3 90.4 + - - +
102B THR* 1.3 64.7 + - - +
103B ALA* 3.5 9.1 + - - +
104B ALA 2.9 21.1 + - - -
105B SER* 3.1 8.9 + - - -
117B ASN* 2.9 21.0 + - + +
118B GLY* 2.8 34.0 + - - -
166B ARG* 3.7 12.7 + - - +
370B HIS* 4.3 1.3 - - - -
412B HIS* 3.8 10.8 - - + -
956B PO4 3.8 7.4 - - - +
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Residues in contact with THR 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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51B ASP* 3.4 4.1 + - - +
101B ASP* 1.3 71.0 - - - +
103B ALA* 1.3 66.3 + - - +
105B SER* 3.0 6.3 + - - -
106B ALA* 3.0 23.5 + - + +
153B ASP* 6.0 0.2 - - - -
154B ALA* 3.6 17.7 - - + -
155B THR* 3.0 29.8 - - - +
166B ARG* 5.9 0.2 - - - -
369B ASP* 3.2 13.2 - - - +
412B HIS* 4.0 1.0 - - - -
451B ZN 2.2 29.1 - - - -
452B MG 3.6 4.3 - - - -
956B PO4 2.4 33.1 + - - -
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Residues in contact with ALA 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 ASP* 3.2 15.9 + - - +
102B THR* 1.3 80.0 - - - +
104B ALA* 1.3 58.6 + - - +
106B ALA* 3.8 2.1 - - - +
107B THR* 2.9 32.2 + - - -
118B GLY* 3.6 16.4 - - - +
119B ALA 3.1 17.9 - - - +
120B LEU* 3.8 14.7 - - + +
154B ALA* 3.6 10.7 - - + +
166B ARG* 3.9 12.1 - - + +
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Residues in contact with ALA 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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88B ALA* 4.0 8.5 - - + -
100B THR* 3.4 16.2 - - - +
101B ASP* 2.9 14.2 + - - +
103B ALA* 1.3 73.8 - - - +
105B SER* 1.3 57.6 + - - +
107B THR* 3.4 2.8 + - - -
108B ALA* 3.0 25.5 + - - +
115B THR* 3.7 22.8 + - + +
116B TYR 3.5 23.6 - - - +
117B ASN* 3.7 7.6 - - - +
118B GLY 4.4 0.2 - - - +
119B ALA 3.7 1.3 + - - -
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Residues in contact with SER 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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86B HIS 5.1 0.7 - - - -
100B THR* 3.4 13.1 + - - -
101B ASP 3.1 12.5 + - - -
102B THR* 3.0 15.8 + - - -
104B ALA* 1.3 74.8 - - - +
106B ALA* 1.3 64.3 + - - +
108B ALA* 3.1 18.4 + - - +
109B TRP* 3.2 15.3 + - - -
369B ASP* 3.3 34.0 + - - +
370B HIS* 4.2 0.3 - - - -
435B GLN* 3.0 24.0 - - - +
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Residues in contact with ALA 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 THR* 3.0 18.9 + - + +
103B ALA 3.8 1.8 - - - +
105B SER* 1.3 74.5 + - - +
107B THR* 1.3 60.8 + - - +
109B TRP* 3.5 31.6 + - + -
110B SER* 2.8 36.3 + - - +
154B ALA 4.1 9.0 - - - +
155B THR* 4.2 7.2 - - - +
158B ALA* 3.6 19.5 - - + -
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Residues in contact with THR 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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103B ALA 2.9 21.9 + - - -
104B ALA 3.5 5.6 - - - -
105B SER 3.2 0.2 - - - -
106B ALA* 1.3 76.4 - - - +
108B ALA* 1.3 55.2 + - - +
110B SER* 4.2 4.7 - - - -
111B THR* 2.7 52.3 + - - +
113B VAL* 3.8 7.2 - - + +
115B THR* 3.8 20.9 - - + -
119B ALA 3.3 7.3 + - - -
120B LEU* 3.4 1.7 - - - -
121B GLY* 3.0 33.7 + - - +
122B VAL 4.2 9.6 - - - +
158B ALA* 4.2 5.1 - - - +
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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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104B ALA 3.0 14.0 + - - +
105B SER* 3.1 11.4 + - - +
107B THR* 1.3 76.4 - - - +
109B TRP* 1.3 57.7 + - - +
112B GLY* 2.9 28.4 + - - -
113B VAL 3.6 13.7 - - - +
114B LYS* 4.8 9.6 - - + -
435B GLN* 3.7 18.6 - - + +
436B THR* 3.5 26.1 - - + -
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Residues in contact with TRP 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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47B LEU* 3.6 16.3 - - + +
49B ILE* 3.8 37.5 - - + -
84B TYR* 4.5 4.0 - - - -
105B SER 3.2 21.2 + - - -
106B ALA* 3.5 32.3 - - + -
108B ALA* 1.3 79.0 - - - +
110B SER* 1.3 69.5 + - - +
111B THR 3.5 0.2 - - - -
132B ILE* 5.5 0.2 - - + -
155B THR* 4.1 15.0 - - + -
159B LEU* 5.3 1.3 - - + -
320B GLN* 3.1 26.2 + - - -
369B ASP* 3.4 34.5 - - + -
435B GLN* 3.5 34.3 + - + +
438B LEU* 3.9 18.6 - - + -
439B PHE* 3.3 25.0 - - - +
442B MET* 3.5 11.3 - - + +
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Residues in contact with SER 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 ALA 2.8 24.7 + - - -
107B THR* 3.2 3.8 + - - -
109B TRP* 1.3 89.0 + - - +
111B THR* 1.3 61.1 + - - +
131B THR* 3.1 4.8 - - - -
132B ILE* 2.7 34.0 + - - -
155B THR 5.3 0.3 + - - -
158B ALA* 3.9 23.0 - - - +
159B LEU* 3.2 28.1 - - - +
439B PHE* 3.2 4.6 - - - -
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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
----------------------------------------------------------
107B THR* 2.7 36.8 + - + +
110B SER* 1.3 78.6 - - - +
112B GLY* 1.3 60.8 + - - +
113B VAL* 3.4 19.6 + - - +
121B GLY* 4.4 14.4 - - - -
129B HIS* 3.4 28.6 - - + +
130B PRO 3.3 25.0 - - - +
131B THR* 4.1 9.6 - - + -
158B ALA 5.1 0.2 - - - +
439B PHE* 3.5 20.2 - - - -
440B TYR* 4.8 1.7 + - - -
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Residues in contact with GLY 112 (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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18A ALA 4.7 0.2 - - - +
20A GLY 3.2 24.3 + - - -
22A ALA 5.8 0.3 + - - -
108B ALA 2.9 16.0 + - - -
111B THR* 1.3 77.7 - - - +
113B VAL* 1.3 58.5 + - - +
436B THR* 3.7 18.9 - - - +
439B PHE* 3.3 24.0 - - - -
440B TYR* 3.8 8.9 - - - -
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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
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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