Contacts of the helix formed by residues 15 - 19 (chain p) in PDB entry 5JPQ
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 PRO 15 (chain p).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9p LEU* 5.0 4.3 - - + -
13p ASN 3.4 2.2 - - - +
14p ALA* 1.3 95.4 - - + +
16p LYS* 1.3 60.1 + - - +
17p SER* 3.0 21.4 + - - +
18p TRP* 3.2 47.7 + - + +
19p MET 4.4 0.9 + - - -
20p LEU* 4.8 2.8 + - - +
38p LEU 5.2 0.7 - - - +
39p ARG* 3.3 48.0 - - - +
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Residues in contact with LYS 16 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3662 A 5.7 2.8 + - - -
14p ALA 4.6 0.4 - - - -
15p PRO* 1.3 69.3 - - - +
17p SER* 1.3 62.8 + - - +
18p TRP 3.1 1.6 - - - -
19p MET* 3.2 32.8 + - + +
20p LEU 5.6 0.4 - - - +
22p LYS* 4.5 22.7 - - - +
109p GLY 5.1 0.6 - - - +
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Residues in contact with SER 17 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15p PRO* 3.5 11.8 - - - +
16p LYS* 1.3 78.9 - - - +
18p TRP* 1.3 77.1 + - - +
19p MET* 3.1 6.7 + - - +
39p ARG 4.2 5.3 + - - -
51p ARG* 4.7 1.6 + - - -
105p TYR* 4.8 3.1 - - - -
109p GLY 3.9 20.6 - - - -
110p ARG* 4.0 3.5 - - - +
111p PHE* 3.3 51.9 + - - +
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Residues in contact with TRP 18 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9p LEU* 4.3 7.0 - - + -
14p ALA* 4.1 15.3 - - + -
15p PRO* 3.2 28.4 + - + +
16p LYS 3.1 1.0 - - - -
17p SER* 1.3 93.3 + - - +
19p MET* 1.3 71.2 + - - +
20p LEU* 2.8 36.6 + - + +
28p ALA* 4.4 4.0 - - + -
29p THR 3.4 27.8 - - - -
31p PRO* 3.7 20.0 - - + -
38p LEU 4.7 2.5 - - - -
39p ARG 4.9 0.8 + - - -
41p SER* 3.0 21.9 + - - -
42p LEU* 3.9 19.2 - - + +
43p PRO* 3.3 26.2 - - + -
46p VAL* 3.9 27.1 - - + +
50p GLU* 5.4 4.2 - - - +
51p ARG* 4.6 8.9 + - - +
111p PHE* 5.3 0.9 - + - -
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Residues in contact with MET 19 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16p LYS* 3.2 37.5 + - + +
17p SER 3.1 4.1 - - - +
18p TRP* 1.3 78.0 - - - +
20p LEU* 1.3 64.1 + - - +
21p ASN 4.0 0.2 + - - -
22p LYS* 5.7 2.0 - - - +
50p GLU* 5.9 2.1 - - - +
51p ARG* 4.4 22.4 + - - +
110p ARG* 3.4 58.3 - - + +
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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