Contacts of the helix formed by residues 6 - 15 (chain T) in PDB entry 4PJO
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 ASN 6 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25S LEU* 5.4 2.1 - - - +
49S GLY* 3.2 7.3 - - - -
50S PHE* 3.0 30.4 + - - +
51S ASP* 5.7 0.2 - - + -
57S VAL* 3.5 4.3 - - - -
4T PRO* 3.8 13.0 + - - +
5T LEU* 1.3 75.9 + - - +
7T PRO* 1.3 76.1 - - + +
8T LYS 3.5 0.9 - - - +
9T PRO* 3.1 19.3 - - + +
10T PHE* 2.9 22.9 + - - +
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Residues in contact with PRO 7 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50S PHE* 3.3 19.1 - - - +
51S ASP* 3.6 23.6 - - + +
55S ASN* 3.7 25.8 - - + +
57S VAL* 3.7 17.7 - - + -
78S MET* 3.6 20.9 - - + -
6T ASN* 1.3 88.5 - - + +
8T LYS* 1.3 65.1 + - - +
10T PHE* 3.0 4.6 + - + +
11T LEU* 3.0 28.5 + - - +
40T MET* 4.0 6.1 - - + -
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Residues in contact with LYS 8 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1263 A 4.7 1.0 - - - +
51S ASP* 5.1 2.0 + - - -
53S TYR* 4.9 7.9 + - - -
7T PRO* 1.3 77.9 - - - +
9T PRO* 1.4 67.0 - - + +
11T LEU* 3.3 9.7 + - + +
12T ASN* 2.9 45.5 + - - +
36T VAL* 5.6 2.2 - - - -
37T ASP 4.3 13.7 - - - -
38T GLY* 4.0 25.7 + - - -
40T MET* 4.0 24.2 - - - +
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Residues in contact with PRO 9 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5T LEU* 4.4 13.0 - - + +
6T ASN* 3.1 36.8 - - + +
8T LYS* 1.4 92.3 - - + +
10T PHE* 1.3 57.6 + - - +
12T ASN* 3.7 11.2 - - + +
13T GLY* 3.0 23.6 + - - -
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Residues in contact with PHE 10 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57S VAL* 4.0 12.3 - - + -
76S ARG* 3.4 55.9 - - + -
77S ILE 3.8 0.7 - - - -
78S MET* 3.5 40.4 - - + -
5T LEU* 4.2 18.1 - - + +
6T ASN 2.9 21.1 + - - +
7T PRO* 3.0 6.9 + - + +
9T PRO* 1.3 75.2 - - - +
11T LEU* 1.3 63.5 + - + +
13T GLY* 3.4 3.0 + - - -
14T LEU* 3.0 55.7 + - + +
72T ILE* 4.2 2.9 - - + -
74T GLY 5.3 0.4 - - - -
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Residues in contact with LEU 11 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78S MET* 4.8 5.8 - - + -
7T PRO 3.0 18.8 + - - +
8T LYS* 3.6 9.2 - - - +
10T PHE* 1.3 76.9 - - + +
12T ASN* 1.3 62.9 + - - +
13T GLY 3.0 1.3 - - - -
14T LEU* 2.9 11.4 + - + +
15T THR* 2.8 30.1 + - - -
33T LEU* 4.3 9.8 - - + +
36T VAL* 3.8 26.2 - - + -
40T MET* 3.8 39.7 - - + -
42T MET* 4.7 5.8 - - + -
72T ILE* 3.9 41.7 - - + -
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Residues in contact with ASN 12 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8T LYS* 2.9 43.8 + - - +
9T PRO* 3.8 9.6 - - + +
10T PHE 3.4 0.2 - - - -
11T LEU* 1.3 76.1 - - - +
13T GLY* 1.3 56.8 + - - +
15T THR* 3.2 16.7 + - - -
36T VAL* 5.7 5.0 - - - +
88b LYS* 3.0 26.9 + - + +
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Residues in contact with GLY 13 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9T PRO 3.0 15.4 + - - -
10T PHE 3.6 4.9 - - - -
11T LEU 3.0 0.2 - - - -
12T ASN* 1.3 77.0 - - - +
14T LEU* 1.3 62.3 + - - +
15T THR 3.0 2.3 + - - -
17T LYS* 3.1 22.9 + - - +
88b LYS* 3.2 14.2 + - - -
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Residues in contact with LEU 14 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10T PHE* 3.0 55.6 + - + +
11T LEU* 2.9 15.3 + - + +
13T GLY* 1.3 70.4 - - - +
15T THR* 1.3 57.5 + - - +
16T GLY 3.6 0.2 - - - -
17T LYS* 2.8 48.2 + - + +
18T PRO 4.9 2.0 - - - +
19T VAL* 3.7 28.9 - - + -
33T LEU* 3.9 9.3 - - + +
72T ILE* 4.5 16.8 - - + -
73T ARG 4.5 5.4 - - - -
74T GLY* 4.3 15.7 - - - -
75T VAL 5.3 0.2 - - - +
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Residues in contact with THR 15 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11T LEU 2.8 18.2 + - - -
12T ASN* 3.2 23.8 + - - -
13T GLY 3.0 2.4 + - - -
14T LEU* 1.3 71.9 - - - +
16T GLY* 1.3 60.5 + - - +
17T LYS 3.1 0.3 + - - -
33T LEU* 2.2 42.5 - - - +
34T VAL* 3.5 24.4 - - - +
35T SER* 5.3 1.8 - - - -
36T VAL* 5.3 5.2 + - - +
88b LYS* 4.0 6.3 - - + +
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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