Contacts of the helix formed by residues 6 - 15 (chain f) 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 f).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25e LEU* 5.4 0.9 - - - +
49e GLY* 3.3 6.9 - - - -
50e PHE* 3.0 31.6 + - - +
51e ASP* 5.7 0.2 - - + -
57e VAL* 3.6 3.4 - - - -
4f PRO* 3.8 22.8 + - - +
5f LEU* 1.3 75.3 - - - +
7f PRO* 1.3 69.5 - - + +
8f LYS 3.5 0.9 - - - +
9f PRO* 3.1 19.4 - - + +
10f PHE* 2.9 28.6 + - - +
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Residues in contact with PRO 7 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50e PHE* 3.2 19.3 - - - +
51e ASP* 3.7 27.4 - - + +
55e ASN* 3.7 24.9 - - + +
57e VAL* 3.8 16.4 - - + -
78e MET* 4.2 12.6 - - + -
6f ASN* 1.3 88.5 - - + +
8f LYS* 1.3 64.7 + - - +
10f PHE* 3.1 5.1 + - + +
11f LEU* 3.0 28.2 + - - +
40f MET* 4.0 11.7 - - + -
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Residues in contact with LYS 8 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1262 A 4.6 1.0 - - - +
53e TYR* 4.9 8.7 + - - -
6f ASN* 4.8 0.2 - - - +
7f PRO* 1.3 78.9 - - - +
9f PRO* 1.4 65.8 - - + +
11f LEU* 3.3 10.1 + - + +
12f ASN* 2.9 45.2 + - - +
36f VAL* 5.6 2.2 - - - -
37f ASP 4.3 13.7 - - - -
38f GLY* 4.0 24.8 + - - -
40f MET* 4.0 24.7 - - - +
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Residues in contact with PRO 9 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4f PRO 5.8 0.4 - - - +
5f LEU* 4.5 13.2 - - + +
6f ASN* 3.1 37.0 - - + +
8f LYS* 1.4 93.2 - - + +
10f PHE* 1.3 56.9 + - - -
12f ASN* 3.9 11.1 - - + +
13f GLY* 3.0 24.1 + - - -
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Residues in contact with PHE 10 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57e VAL* 4.0 12.1 - - + -
76e ARG* 3.6 52.9 - - + -
77e ILE 4.1 0.7 - - - -
78e MET* 3.7 39.0 - - + -
5f LEU* 4.1 19.0 - - + +
6f ASN 2.9 24.0 + - - +
7f PRO* 3.3 6.5 - - + +
9f PRO* 1.3 72.2 - - - +
11f LEU* 1.3 62.4 + - + +
13f GLY* 3.4 3.2 + - - -
14f LEU* 3.1 61.2 + - + +
72f ILE* 4.2 5.2 - - + -
74f GLY 4.9 1.1 - - - -
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Residues in contact with LEU 11 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78e MET* 3.5 33.0 - - + -
7f PRO 3.0 16.6 + - - +
8f LYS* 3.6 9.4 - - - +
10f PHE* 1.3 77.8 - - + +
12f ASN* 1.3 57.3 + - - +
13f GLY 3.0 1.6 - - - -
14f LEU* 2.8 9.7 + - + +
15f THR* 2.7 37.9 + - - +
33f LEU* 4.3 8.5 - - + +
36f VAL* 3.8 24.5 - - + -
40f MET* 3.7 26.0 - - + -
42f MET* 4.7 4.5 - - + -
72f ILE* 3.8 33.0 - - + -
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Residues in contact with ASN 12 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8f LYS* 2.9 42.5 + - - +
9f PRO* 3.9 9.7 - - + +
11f LEU* 1.3 76.1 - - - +
13f GLY* 1.3 62.5 + - - +
15f THR* 3.2 30.0 + - - +
36f VAL* 5.7 3.6 - - - +
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Residues in contact with GLY 13 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9f PRO 3.0 15.0 + - - -
10f PHE 3.6 4.9 - - - -
11f LEU 3.0 0.2 - - - -
12f ASN* 1.3 78.8 - - - +
14f LEU* 1.3 61.9 + - - +
15f THR 3.1 8.8 + - - +
17f LYS* 3.1 22.2 + - - +
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Residues in contact with LEU 14 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10f PHE* 3.1 55.1 + - + +
11f LEU* 2.8 15.0 + - + +
13f GLY* 1.3 69.3 - - - +
15f THR* 1.3 58.3 + - - +
16f GLY 3.3 0.2 + - - -
17f LYS* 2.8 51.4 + - + +
18f PRO 5.4 0.2 - - - +
19f VAL* 3.5 27.6 - - + -
33f LEU* 4.0 9.2 - - + +
72f ILE* 4.5 11.7 - - + -
73f ARG 4.3 3.1 - - - -
74f GLY* 4.1 19.5 - - - +
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Residues in contact with THR 15 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11f LEU 2.7 26.2 + - - +
12f ASN* 3.2 27.5 + - - +
13f GLY 3.1 10.4 + - - +
14f LEU* 1.3 74.3 - - - +
16f GLY* 1.3 58.8 + - - +
17f LYS* 3.4 3.8 + - - +
33f LEU* 3.8 21.7 - - + +
34f VAL 4.3 13.9 - - - +
35f SER* 5.0 2.2 - - - -
36f VAL* 4.6 13.0 - - + +
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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