Contacts of the helix formed by residues 97 - 112 (chain B) in PDB entry 2PX7
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 97 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95B PHE 4.0 2.2 + - - -
96B VAL* 1.3 78.4 - - - +
98B ARG* 1.3 64.0 + - - +
99B GLY* 3.7 4.0 + - - -
100B LEU* 3.3 23.5 + - - +
101B VAL* 3.3 22.8 + - - +
189B GLU* 3.7 19.7 + - - +
191B THR* 5.3 4.4 + - - -
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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
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38B ALA* 5.5 7.2 - - - +
97B SER* 1.3 72.0 - - - +
99B GLY* 1.3 66.1 + - - +
101B VAL* 3.4 8.5 + - - +
102B ALA* 3.0 25.2 + - - +
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Residues in contact with GLY 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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97B SER* 3.3 5.6 + - - -
98B ARG* 1.3 79.2 - - - +
100B LEU* 1.3 55.7 + - - +
102B ALA* 3.5 5.1 + - - +
103B ARG* 2.9 45.2 + - - +
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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
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96B VAL* 3.8 23.3 - - + -
97B SER* 3.3 23.0 + - - +
98B ARG 3.2 0.6 - - - -
99B GLY* 1.3 73.5 - - - +
101B VAL* 1.3 65.2 + - - +
103B ARG* 3.2 11.5 + - + +
104B VAL* 3.0 27.9 + - + +
116B PRO* 3.6 28.7 - - + -
145B GLN* 4.9 2.0 - - - +
146B THR 4.4 8.1 - - - +
147B PRO* 4.3 4.5 - - + -
187B GLU 3.8 15.0 - - - +
188B GLY* 4.2 2.2 - - - -
189B GLU* 3.9 22.0 - - + +
192B ALA* 3.9 22.2 - - + -
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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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1B MET* 3.9 28.3 - - + -
38B ALA 4.3 12.8 - - - +
39B PHE* 3.7 31.9 - - + -
87B LEU* 3.9 8.3 - - + +
96B VAL* 3.5 20.0 - - + +
97B SER 3.3 16.0 + - - +
98B ARG* 3.4 8.3 + - - +
100B LEU* 1.3 75.5 - - - +
102B ALA* 1.3 57.6 + - - +
104B VAL* 3.9 1.6 - - - +
105B LEU* 2.9 28.8 + - - +
147B PRO* 4.5 8.1 - - + -
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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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1B MET* 6.3 0.4 - - - -
98B ARG 3.0 18.1 + - - +
99B GLY* 3.9 5.8 - - - +
101B VAL* 1.3 73.8 - - - +
103B ARG* 1.3 61.8 + - - +
105B LEU* 4.1 7.6 - - - +
106B GLU* 2.9 33.5 + - - +
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Residues in contact with ARG 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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99B GLY* 2.9 33.5 + - - +
100B LEU* 3.4 18.6 - - + +
102B ALA* 1.3 76.7 - - - +
104B VAL* 1.3 60.8 + - - +
106B GLU* 3.9 14.2 - - - +
107B ALA* 3.2 24.6 + - - +
110B ARG* 5.1 0.2 + - - -
186B VAL* 3.8 17.8 - - + +
187B GLU* 2.7 62.4 + - - +
188B GLY 3.5 7.3 + - - -
189B GLU* 3.2 27.3 + - - -
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Residues in contact with VAL 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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87B LEU* 3.9 11.0 - - + -
100B LEU* 3.0 29.5 + - + +
101B VAL 3.9 2.9 - - - +
103B ARG* 1.3 73.3 - - - +
105B LEU* 1.3 57.1 + - - +
107B ALA* 3.3 4.0 + - - +
108B ALA* 2.8 32.7 + - - +
114B ALA* 3.7 9.8 - - - +
116B PRO* 3.9 8.3 - - + -
147B PRO* 3.3 36.3 - - + +
149B GLY* 3.5 22.9 - - - +
186B VAL* 3.8 23.6 - - + -
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Residues in contact with LEU 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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1B MET* 3.8 36.1 - - + +
3B VAL* 3.2 37.0 - - + -
85B LEU* 4.4 13.7 - - + -
86B VAL 6.1 0.4 - - - +
87B LEU* 4.3 16.1 - - + +
101B VAL 2.9 19.3 + - - +
102B ALA* 4.1 6.1 - - - +
104B VAL* 1.3 77.7 - - - +
106B GLU* 1.3 55.9 + - - +
108B ALA* 3.2 5.5 + - + +
109B GLN* 2.9 53.6 + - + +
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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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102B ALA 2.9 23.6 + - - +
103B ARG* 3.9 13.7 - - - +
105B LEU* 1.3 75.3 - - - +
107B ALA* 1.3 57.1 + - - +
109B GLN* 3.4 17.6 + - - +
110B ARG* 2.6 69.3 + - + +
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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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103B ARG 3.2 16.1 + - - +
106B GLU* 1.3 78.5 - - - +
108B ALA* 1.3 60.3 + - - +
110B ARG* 3.5 26.9 - - - +
111B SER* 3.0 34.8 + - - -
114B ALA* 3.6 15.5 - - + -
184B ALA* 5.1 5.6 - - + -
186B VAL* 3.5 19.1 - - + -
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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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85B LEU* 4.2 13.5 - - + -
86B VAL 5.5 0.2 - - - +
104B VAL 2.8 17.6 + - - +
105B LEU* 3.5 9.4 - - + +
107B ALA* 1.3 76.6 - - - +
109B GLN* 1.3 57.4 + - - +
112B GLY* 2.6 34.7 + - - +
113B ALA 4.3 3.1 - - - +
114B ALA* 3.7 6.2 - - - +
149B GLY* 3.6 31.9 - - - +
150B PHE* 3.9 4.0 - - - +
151B PHE* 3.6 3.8 - - - -
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Residues in contact with GLN 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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1B MET 5.4 4.6 + - - -
2B GLU 5.6 0.6 + - - -
3B VAL* 5.5 0.2 - - - +
85B LEU* 3.6 30.9 - - + +
105B LEU* 2.9 38.2 + - + +
106B GLU* 3.6 15.4 - - - +
108B ALA* 1.3 75.8 - - - +
110B ARG* 1.3 61.3 + - + +
151B PHE* 3.7 20.6 - - - -
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Residues in contact with ARG 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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103B ARG 5.1 0.2 + - - -
106B GLU* 2.6 68.6 + - + +
107B ALA* 3.5 29.4 - - - +
108B ALA 3.2 0.2 - - - -
109B GLN* 1.3 78.9 - - + +
111B SER* 1.3 61.0 + - - +
151B PHE* 5.2 1.0 - - - -
186B VAL* 4.8 5.5 - - - +
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Residues in contact with SER 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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107B ALA 3.0 17.8 + - - -
110B ARG* 1.3 81.1 - - - +
112B GLY* 1.3 51.9 + - - +
113B ALA 3.3 20.3 + - - -
151B PHE* 4.4 3.6 - - - -
181B TYR* 2.6 32.0 + - - -
182B PRO* 4.9 3.9 - - - +
184B ALA* 3.6 15.4 - - - +
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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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108B ALA 2.6 24.0 + - - -
111B SER* 1.3 72.2 + - - +
113B ALA* 1.3 60.5 + - - +
149B GLY 4.5 0.2 - - - -
150B PHE* 3.2 3.9 - - - -
151B PHE* 3.0 50.8 + - - -
154B LEU* 3.5 10.0 - - - +
181B TYR* 3.9 5.2 - - - -
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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