Contacts of the helix formed by residues 69 - 81 (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 THR 69 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11B GLY* 3.6 9.0 - - - -
67B GLY 4.0 0.2 - - - -
68B ALA* 1.3 88.9 - - + +
70B ARG* 1.3 66.7 + - - +
71B GLN* 3.6 9.1 + - - +
72B ALA* 3.1 23.0 + - + +
73B SER* 3.0 23.2 + - - -
168B GLU* 4.2 19.4 + - - +
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Residues in contact with ARG 70 (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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8B PRO* 3.8 24.4 - - + +
11B GLY* 3.5 24.7 - - - +
69B THR* 1.3 73.3 - - - +
71B GLN* 1.3 79.3 + - - +
73B SER* 3.1 8.4 + - - -
74B VAL* 2.9 40.8 + - - +
88B VAL* 4.3 4.6 - - - +
90B ASP* 3.8 22.9 + - - -
148B GLN* 5.6 1.2 + - - -
169B ALA 4.5 2.2 + - - -
170B SER 3.8 24.2 + - - -
171B ASP* 4.0 10.1 - - - +
172B ASP* 2.6 40.0 + - - +
194B LYS* 6.0 4.0 - - - +
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Residues in contact with GLN 71 (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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69B THR* 3.2 9.1 + - - +
70B ARG* 1.3 92.1 - - - +
72B ALA* 1.3 58.2 + - - +
74B VAL* 3.2 7.2 + - - +
75B ALA* 2.9 25.9 + - + +
159B HIS* 3.5 20.8 + - + +
162B ALA* 3.8 17.2 - - - +
163B ARG* 5.2 4.2 - - - +
167B LEU 2.9 24.2 + - - -
168B GLU* 3.4 8.3 - - - +
169B ALA* 3.0 35.3 + - - +
171B ASP 6.1 0.2 - - - +
175B LEU* 3.8 14.0 - - + +
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Residues in contact with ALA 72 (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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67B GLY* 4.1 16.4 - - - -
68B ALA* 4.2 3.6 - - + +
69B THR* 3.1 22.3 + - - +
71B GLN* 1.3 79.7 - - - +
73B SER* 1.3 58.0 + - - +
75B ALA* 3.5 8.8 + - - +
76B ARG* 3.1 33.1 + - - +
163B ARG* 6.3 0.9 - - - +
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Residues in contact with SER 73 (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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8B PRO* 3.8 18.4 - - - -
10B ALA* 3.5 11.8 - - - +
11B GLY 3.7 2.4 + - - -
48B ALA* 4.0 10.3 - - - +
66B GLY* 3.3 7.9 - - - -
67B GLY 2.8 25.7 + - - +
69B THR 3.0 11.8 + - - -
70B ARG* 3.1 11.4 + - - -
72B ALA* 1.3 74.5 - - - +
74B VAL* 1.3 65.4 + - - +
76B ARG* 3.4 5.1 + - - +
77B LEU* 3.0 29.0 + - - +
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Residues in contact with VAL 74 (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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6B LEU* 4.2 16.4 - - + -
8B PRO* 3.7 24.7 - - + -
70B ARG* 2.9 40.4 + - - +
71B GLN* 3.2 7.6 + - - +
73B SER* 1.3 75.4 - - - +
75B ALA* 1.3 63.3 + - - +
77B LEU* 3.2 8.1 + - - +
78B LEU* 2.9 25.0 + - + +
88B VAL* 3.9 9.0 - - + -
155B LEU* 4.3 2.9 - - + -
159B HIS* 3.4 26.2 - - + +
172B ASP* 3.5 9.9 - - - +
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Residues in contact with ALA 75 (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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71B GLN* 2.9 14.4 + - + +
72B ALA* 3.6 12.8 - - - +
73B SER 3.3 0.2 - - - -
74B VAL* 1.3 77.9 - - - +
76B ARG* 1.3 60.9 + - + +
78B LEU* 3.4 13.3 + - - +
79B GLU* 3.5 16.7 + - - +
159B HIS* 3.8 21.7 + - + +
163B ARG* 4.3 24.2 - - - +
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Residues in contact with ARG 76 (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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64B LEU* 4.0 13.7 - - + +
65B GLU* 3.3 42.4 + - - +
66B GLY 3.6 25.5 + - - -
67B GLY* 3.7 12.5 - - - +
72B ALA* 3.1 15.5 + - - +
73B SER* 3.6 7.4 - - - +
74B VAL 3.3 0.2 - - - -
75B ALA* 1.3 76.0 - - + +
77B LEU* 1.3 61.1 + - + +
79B GLU* 3.3 26.5 + - + +
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Residues in contact with LEU 77 (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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6B LEU* 3.9 22.7 - - + -
7B ILE 3.7 41.7 - - - +
8B PRO* 3.8 6.1 - - + -
46B LEU* 3.6 24.4 - - + +
47B VAL 3.6 25.4 - - - +
48B ALA* 3.6 11.4 - - + +
64B LEU* 3.9 19.1 - - + -
73B SER 3.0 22.7 + - - +
74B VAL* 3.2 4.9 + - - +
76B ARG* 1.3 76.0 - - + +
78B LEU* 1.3 62.6 + - - +
80B ALA* 3.0 13.2 + - - +
81B ALA* 3.2 9.4 + - - +
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Residues in contact with LEU 78 (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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6B LEU* 3.8 20.4 - - + +
74B VAL* 2.9 17.0 + - + +
75B ALA* 3.6 7.0 - - - +
76B ARG 3.3 0.2 - - - -
77B LEU* 1.3 72.9 - - - +
79B GLU* 1.3 59.2 + - - +
80B ALA 3.3 0.5 + - - -
81B ALA* 3.4 7.9 + - + +
86B VAL* 4.6 2.0 - - + -
152B THR* 4.0 26.9 - - + +
155B LEU* 3.8 26.5 - - + +
156B ARG* 2.3 57.2 + - + +
159B HIS* 3.5 39.5 - - + -
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Residues in contact with GLU 79 (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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64B LEU* 5.8 0.2 - - + -
75B ALA 3.5 10.6 + - - +
76B ARG* 3.3 20.6 + - + +
77B LEU 3.2 0.6 - - - -
78B LEU* 1.3 77.6 - - - +
80B ALA* 1.3 61.0 + - + +
81B ALA 4.6 1.7 - - - +
156B ARG* 3.9 8.7 + - - +
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Residues in contact with ALA 80 (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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44B GLU* 4.1 6.8 - - - +
46B LEU* 3.9 17.0 - - + +
62B VAL* 5.8 1.3 - - + -
64B LEU* 3.8 26.0 - - + -
77B LEU 3.0 9.2 + - - +
79B GLU* 1.3 77.5 - - + +
81B ALA* 1.3 64.3 + - - +
82B SER* 3.3 9.2 + - - -
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Residues in contact with ALA 81 (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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4B SER* 3.9 13.7 - - - +
6B LEU* 4.0 24.0 - - + -
44B GLU* 3.4 7.6 - - - -
46B LEU* 3.6 2.6 - - - +
77B LEU 3.2 6.3 + - - +
78B LEU* 3.4 15.7 + - + +
79B GLU 4.6 1.0 - - - +
80B ALA* 1.3 74.3 - - - +
82B SER* 1.3 58.9 + - - +
83B LEU 3.7 1.3 - - - -
86B VAL* 5.0 0.2 - - + -
152B THR* 4.2 16.1 - - + +
156B ARG* 2.9 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