Contacts of the helix formed by residues 101 - 112 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A THR* 1.3 91.7 + - - +
102A THR* 1.3 61.4 + - - +
103A ALA* 3.5 2.7 - - - +
104A ALA* 2.8 25.6 + - - +
105A SER* 3.0 9.6 + - - -
117A ASN* 2.9 18.5 + - + +
118A GLY* 2.9 27.7 + - - -
166A ARG* 3.3 24.1 - - - -
370A HIS* 4.3 1.1 - - - -
412A HIS* 3.7 9.9 - - + -
656A PO4 3.7 8.0 + - - +
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Residues in contact with THR 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ASP* 3.3 1.9 + - - +
101A ASP* 1.3 72.8 - - - +
103A ALA* 1.3 63.5 + - - +
105A SER* 3.1 6.5 + - - -
106A ALA* 2.9 30.0 + - - +
153A ASP* 5.1 4.3 - - - +
154A ALA* 3.2 20.8 - - + +
155A THR* 3.2 21.0 + - - +
166A ARG* 4.6 3.6 - - - +
369A ASP* 3.0 13.4 + - - +
412A HIS* 3.9 2.0 - - - -
451A ZN 3.0 19.9 - - - -
656A PO4 3.1 31.7 + - - +
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Residues in contact with ALA 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A ASP* 3.2 14.3 + - - +
102A THR* 1.3 81.9 - - - +
104A ALA* 1.3 57.0 + - - +
106A ALA* 3.9 1.3 - - - +
107A THR* 2.8 33.3 + - - -
118A GLY 3.8 7.9 - - - -
119A ALA 3.2 17.4 - - - +
120A LEU* 3.7 16.5 - - + +
154A ALA* 3.8 9.6 - - + -
166A ARG* 3.7 19.1 - - + -
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Residues in contact with ALA 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A ALA* 4.0 3.4 - - + -
100A THR* 3.4 11.7 - - - +
101A ASP* 2.8 19.8 + - - +
103A ALA* 1.3 73.9 - - - +
105A SER* 1.3 57.8 + - - +
107A THR* 3.4 3.8 + - - -
108A ALA* 3.0 25.6 + - - +
115A THR* 3.6 28.3 + - + +
116A TYR 3.5 26.0 - - - +
117A ASN* 3.8 4.7 - - - +
118A GLY 4.4 0.2 - - - +
119A ALA 3.7 1.3 + - - -
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Residues in contact with SER 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A HIS 5.2 0.4 - - - -
100A THR* 3.3 17.6 + - - +
101A ASP 3.0 13.5 + - - -
102A THR* 3.1 11.3 + - - -
104A ALA* 1.3 76.3 - - - +
106A ALA* 1.3 64.2 + - - +
108A ALA* 3.0 17.1 + - - +
109A TRP* 3.2 14.6 + - - -
369A ASP* 3.3 32.9 + - - +
435A GLN* 3.1 24.6 - - - +
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Residues in contact with ALA 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A THR* 2.9 20.1 + - - +
103A ALA 3.9 1.6 - - - +
105A SER* 1.3 76.1 + - - +
107A THR* 1.3 55.9 + - - +
109A TRP* 3.4 33.2 + - + -
110A SER* 2.7 34.8 + - - -
154A ALA 4.2 1.3 - - - +
155A THR* 4.1 14.4 - - - -
158A ALA* 3.6 21.1 - - + -
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Residues in contact with THR 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ALA 2.8 23.2 + - - -
104A ALA 3.5 5.4 - - - -
106A ALA* 1.3 77.7 - - - +
108A ALA* 1.3 57.7 + - - +
110A SER* 3.1 6.9 + - - -
111A THR* 2.8 48.0 + - + +
113A VAL* 4.1 5.8 - - + +
115A THR* 3.8 19.7 - - + -
119A ALA 3.2 8.1 + - - -
120A LEU* 3.5 3.5 - - - +
121A GLY* 3.1 34.6 + - - +
122A VAL 3.9 10.5 - - - +
158A ALA* 4.6 2.1 - - - +
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Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ALA 3.0 13.3 + - - +
105A SER 3.0 11.3 + - - +
107A THR* 1.3 76.3 - - - +
109A TRP* 1.3 58.2 + - - +
112A GLY* 2.8 30.5 + - - -
113A VAL 3.5 14.1 - - - +
114A LYS* 5.0 8.7 - - + +
435A GLN* 3.7 21.5 - - + +
436A THR* 3.8 21.1 - - + -
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Residues in contact with TRP 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LEU* 3.6 15.3 - - + +
49A ILE* 3.8 38.4 - - + -
84A TYR* 4.4 4.7 - - - -
105A SER 3.2 19.6 + - - -
106A ALA* 3.4 35.0 + - + -
108A ALA* 1.3 78.6 - - - +
110A SER* 1.3 69.5 + - - +
155A THR* 4.0 13.7 - - + -
158A ALA* 6.1 0.2 - - + -
159A LEU* 4.6 1.5 - - + +
320A GLN* 3.0 24.3 + - - -
369A ASP* 3.5 35.0 - - + -
435A GLN* 3.6 31.1 + - + +
438A LEU* 3.8 19.3 - - + -
439A PHE* 3.1 27.0 - - - +
442A MET* 3.5 10.5 - - + +
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Residues in contact with SER 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ALA 2.7 22.2 + - - -
107A THR* 3.1 13.5 + - - -
109A TRP* 1.3 86.0 - - - +
111A THR* 1.3 62.2 + - - +
131A THR* 3.0 7.4 - - - -
132A ILE* 2.8 33.5 + - - -
158A ALA* 3.7 15.1 + - - +
159A LEU* 3.7 28.0 - - - -
439A PHE* 3.4 4.8 - - - -
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Residues in contact with THR 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A THR* 2.8 35.7 + - + +
110A SER* 1.3 89.5 - - - +
112A GLY* 1.3 62.9 + - - +
113A VAL* 3.3 19.6 + - - +
121A GLY* 4.5 7.6 - - - -
129A HIS* 3.6 26.7 - - + +
130A PRO 3.5 18.0 - - - +
131A THR* 4.2 8.5 - - + -
439A PHE* 3.3 25.9 - - - -
440A TYR* 4.8 1.6 + - - -
19B PRO* 5.7 0.2 - - - +
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Residues in contact with GLY 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ALA 2.8 16.4 + - - -
111A THR* 1.3 79.6 - - - +
113A VAL* 1.3 59.4 + - - +
436A THR* 3.8 13.9 - - - +
439A PHE* 3.3 22.8 - - - -
440A TYR* 3.7 10.6 - - - -
20B GLY 3.1 25.1 + - - -
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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