Contacts of the strand formed by residues 14 - 19 (chain q) 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 THR 14 (chain q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12q HIS 3.9 2.1 + - - -
13q GLU* 1.3 76.8 + - - +
15q VAL* 1.3 62.2 + - - +
26q HIS* 3.3 35.4 - - + +
27q GLY 3.3 10.8 - - - +
28q THR* 2.7 24.3 + - - +
71q PRO* 3.5 21.2 - - - +
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Residues in contact with VAL 15 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10q LEU* 5.0 1.1 - - + -
13q GLU* 4.3 7.0 - - + +
14q THR* 1.3 78.9 - - - +
16q THR* 1.3 66.3 + - - +
17q ILE* 4.0 20.4 - - + -
25q VAL 3.9 0.2 - - - +
26q HIS* 3.4 7.6 + - - -
27q GLY 2.8 35.4 + - - +
29q ILE* 3.8 40.2 - - + -
40q LEU* 4.1 4.9 - - + -
68q PHE* 4.2 7.0 - - + -
69q ILE 3.6 10.5 - - - +
70q LEU* 4.0 23.1 - - + -
71q PRO* 4.2 7.0 - - + -
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Residues in contact with THR 16 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15q VAL* 1.3 71.8 - - - +
17q ILE* 1.3 67.7 + - - +
18q GLU* 5.1 0.7 - - + -
24q GLN* 4.0 21.8 - - + +
25q VAL 3.1 14.1 - - - +
26q HIS* 3.1 25.9 + - + +
67q TYR 3.9 0.2 - - - +
68q PHE 3.6 0.3 - - - -
69q ILE* 2.6 62.8 + - + +
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Residues in contact with ILE 17 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15q VAL* 4.0 14.8 - - + -
16q THR* 1.3 77.2 - - - +
18q GLU* 1.3 67.4 + - - +
19q LEU* 3.6 23.6 - - + +
23q THR 3.9 0.5 - - - +
24q GLN* 3.4 4.5 - - - +
25q VAL* 2.7 45.1 + - + +
38q THR* 4.0 17.3 - - + -
40q LEU* 4.0 18.4 - - + -
60q ILE* 4.2 7.0 - - + -
65q ILE* 4.0 17.0 - - + -
67q TYR 3.3 9.4 - - - +
68q PHE* 3.7 32.3 - - + -
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Residues in contact with GLU 18 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1364 G 3.0 44.2 + - - +
16q THR* 5.1 1.5 - - + +
17q ILE* 1.3 76.3 - - - +
19q LEU* 1.3 59.1 + - - +
23q THR 3.7 4.9 - - - +
24q GLN* 3.9 21.9 + - + +
65q ILE* 3.8 0.7 - - - -
66q ARG* 2.8 30.7 + - - -
67q TYR* 2.9 38.0 + - + +
69q ILE* 3.8 8.4 - - + +
94r ARG* 2.4 38.7 + - - -
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Residues in contact with LEU 19 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1364 G 3.3 16.1 - - - +
78p VAL* 4.1 21.1 - - + -
79p SER* 5.4 3.4 - - - -
17q ILE* 3.6 24.7 - - + +
18q GLU* 1.3 80.2 - - - +
20q LYS* 1.3 61.9 + - - +
21q ASN* 3.0 17.3 - - - +
22q GLY* 2.9 17.8 + - - -
23q THR* 3.0 36.3 + - + +
25q VAL* 4.5 10.3 - - + -
45q MET* 6.3 0.4 - - - -
58q LEU* 6.1 0.2 - - + -
60q ILE* 4.3 20.4 - - + -
64q ASN* 3.2 21.5 - - + +
65q ILE* 4.3 4.0 - - - -
66q ARG* 4.2 0.2 - - - -
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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