Contacts of the helix formed by residues 95 - 109 (chain B) in PDB entry 2PQA
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 95 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A ASN* 2.9 26.4 + - - +
156A THR* 4.8 0.9 + - - +
93B PRO 3.4 3.3 + - - +
94B PHE* 1.3 72.8 - - - +
96B LEU* 1.3 62.1 + - - +
97B GLY* 3.1 8.1 + - - -
98B LEU* 3.1 45.7 + - + +
99B TYR* 3.2 19.2 + - - +
114C SER 5.3 4.2 - - - +
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Residues in contact with LEU 96 (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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28B VAL* 4.1 36.3 - - + +
29B GLY* 4.3 2.0 - - - -
30B ARG* 4.0 27.4 - - + +
44B SER* 3.5 24.0 - - - +
45B ASP 3.8 10.1 - - - +
46B GLY* 3.8 13.7 - - - +
66B ILE* 4.2 9.4 - - + -
94B PHE* 3.1 26.1 + - + +
95B ASP* 1.3 71.1 + - - +
97B GLY* 1.3 58.7 + - - +
99B TYR* 3.1 10.1 + - + +
100B ASN* 2.9 28.4 + - - +
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Residues in contact with GLY 97 (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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46B GLY* 3.9 19.8 - - - +
95B ASP* 3.1 7.0 + - - -
96B LEU* 1.3 77.8 - - - +
98B LEU* 1.3 56.6 + - - +
100B ASN* 3.3 7.6 + - - +
101B GLU* 3.1 30.7 + - - +
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Residues in contact with LEU 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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156A THR* 3.8 9.9 - - + +
160A LEU* 5.8 1.4 - - - +
95B ASP* 3.1 37.3 + - + +
97B GLY* 1.3 71.3 - - - +
99B TYR* 1.3 61.4 + - - +
100B ASN 3.2 0.4 - - - -
101B GLU* 3.2 21.7 + - + +
102B ALA* 2.9 28.1 + - - +
145C LYS* 5.1 22.2 - - - +
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Residues in contact with TYR 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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155A PHE* 3.6 30.5 - + - -
156A THR* 3.7 24.3 - - + +
159A ILE* 4.4 11.2 - - + -
11B ARG* 2.8 38.4 + - - +
12B ILE 5.2 3.0 + - - -
26B CYS 4.8 1.4 + - - -
28B VAL* 3.3 37.0 + - + +
46B GLY 6.3 0.2 - - - -
94B PHE* 3.5 27.1 - + + -
95B ASP 3.2 5.9 + - - -
96B LEU* 3.1 18.3 + - + +
98B LEU* 1.3 76.7 - - - +
100B ASN* 1.3 59.5 + - - +
102B ALA* 3.2 5.4 + - + +
103B VAL* 2.9 43.7 + - + +
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Residues in contact with ASN 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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13B ASN* 2.8 39.0 + - - +
45B ASP* 4.5 1.9 - - - +
46B GLY* 3.8 25.2 + - - +
47B GLU* 4.2 19.3 + - - +
96B LEU 2.9 11.1 + - - +
97B GLY 3.3 10.3 + - - +
98B LEU 3.2 0.2 - - - -
99B TYR* 1.3 78.4 - - + +
101B GLU* 1.3 66.4 + - - +
103B VAL* 3.2 7.3 + - - +
104B LYS* 3.1 41.6 + - - +
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Residues in contact with GLU 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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160A LEU* 6.3 0.4 - - + -
97B GLY 3.1 18.1 + - - +
98B LEU* 3.2 27.1 + - + +
100B ASN* 1.3 74.9 - - - +
102B ALA* 1.3 63.8 + - - +
104B LYS* 2.9 38.1 + - - +
105B ILE* 3.2 33.6 + - + +
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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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156A THR* 3.8 19.3 - - + +
159A ILE* 4.5 18.8 - - + +
160A LEU* 4.0 26.6 - - + +
98B LEU 2.9 13.0 + - - +
99B TYR* 3.3 10.8 - - + +
101B GLU* 1.3 76.1 - - - +
103B VAL* 1.3 60.8 + - - +
105B ILE* 3.4 4.8 + - - +
106B ILE* 3.2 27.5 + - - +
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Residues in contact with VAL 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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11B ARG* 3.7 29.6 - - + +
12B ILE 4.6 4.3 - - - +
13B ASN* 3.9 26.9 - - + +
16B MET* 4.2 4.5 - - - -
99B TYR* 2.9 48.5 + - + +
100B ASN* 3.2 12.5 + - - +
102B ALA* 1.3 73.3 - - - +
104B LYS* 1.3 67.2 + - - +
106B ILE* 3.0 20.1 + - + +
107B HIS* 3.2 26.0 + - + -
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Residues in contact with LYS 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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13B ASN* 4.5 11.2 - - - +
16B MET* 5.3 6.1 - - + -
47B GLU* 5.3 6.1 + - - +
100B ASN* 3.1 35.5 + - - +
101B GLU* 2.9 36.6 + - - +
103B VAL* 1.3 75.9 - - - +
105B ILE* 1.3 59.2 + - + +
107B HIS* 3.1 7.5 + - - +
108B ASP* 2.9 39.3 + - - +
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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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160A LEU* 3.8 23.1 - - + -
163A ILE* 3.6 31.3 - - + +
167A MET* 6.2 0.7 - - + -
101B GLU* 3.2 21.4 + - + +
102B ALA* 3.6 8.1 - - - +
103B VAL 3.2 0.2 - - - -
104B LYS* 1.3 74.5 - - + +
106B ILE* 1.3 58.0 + - - +
108B ASP* 3.3 5.8 + - - +
109B PHE* 2.9 49.9 + - + +
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Residues in contact with ILE 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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159A ILE* 3.6 34.8 - - + -
163A ILE* 4.0 6.5 - - + -
11B ARG* 4.6 18.6 - - + +
102B ALA 3.2 15.8 + - - +
103B VAL* 3.0 15.7 + - + +
105B ILE* 1.3 75.1 - - - +
107B HIS* 1.3 78.3 + - + +
109B PHE 3.4 2.9 - - - +
110B PRO* 3.3 25.3 - - - +
113B TYR* 3.7 46.2 - - + +
115B LEU* 4.2 16.4 - - + +
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Residues in contact with HIS 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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10B SER* 4.3 8.7 - - - -
11B ARG 2.5 29.7 + - - -
12B ILE* 4.2 3.4 - - + -
16B MET* 3.4 34.6 - - + -
20B PHE* 3.7 30.8 - + - -
103B VAL* 3.2 23.9 + - + -
104B LYS 3.1 7.1 + - - +
106B ILE* 1.3 87.8 - - + +
108B ASP* 1.3 68.3 + - - +
110B PRO* 3.6 10.9 - - - +
115B LEU* 4.5 12.6 - - + +
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Residues in contact with ASP 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 LYS* 2.9 26.6 + - - +
105B ILE* 3.3 2.6 + - - +
107B HIS* 1.3 82.8 - - - +
109B PHE* 1.3 87.3 + - + +
110B PRO* 3.4 6.1 - - - +
111B GLN* 4.3 2.3 + - - +
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Residues in contact with PHE 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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163A ILE* 4.9 9.9 - - + +
167A MET* 5.2 7.2 - - + -
105B ILE* 2.9 37.5 + - + +
106B ILE* 3.4 5.8 - - - +
107B HIS 3.4 0.4 - - - -
108B ASP* 1.3 98.7 - - + +
110B PRO* 1.3 64.9 - - - +
111B GLN* 3.1 19.7 - - - -
112B PHE* 2.9 37.0 + + + +
113B TYR* 3.4 8.7 + - - +
44C GLN* 4.0 38.1 - - + -
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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