Contacts of the strand formed by residues 994 - 997 (chain Q) in PDB entry 2J59
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 LEU 994 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49E ILE* 3.8 26.2 - - + +
50E GLY* 5.5 0.7 - - - -
993Q CYS* 1.3 76.1 - - - +
995Q ILE* 1.3 62.5 + - - +
1009Q ARG* 4.3 3.6 - - - +
1010Q LEU* 3.6 1.9 - - - -
1011Q THR* 2.8 49.2 + - + +
1049Q ASN* 3.9 22.0 - - - +
1052Q LEU* 3.6 45.3 - - + +
1053Q ILE* 4.0 19.5 - - + -
1056Q ARG* 4.3 19.5 - - - -
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Residues in contact with ILE 995 (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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46E ILE* 3.7 11.0 - - - +
47E PRO 5.5 0.3 - - - +
49E ILE* 5.8 7.6 + - - +
993Q CYS* 4.6 9.4 - - - +
994Q LEU* 1.3 77.2 - - - +
996Q ASP* 1.3 69.4 + - - +
1008Q PHE* 3.6 28.9 - - + -
1009Q ARG* 3.3 12.3 - - - +
1010Q LEU* 4.5 8.5 - - + -
1031Q ILE* 3.8 25.1 - - + +
1034Q ILE* 3.7 31.6 - - + -
1035Q GLN* 3.7 32.7 - - + +
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Residues in contact with ASP 996 (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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46E ILE* 3.4 28.0 + - - +
47E PRO 5.1 0.7 - - - -
48E THR* 4.1 27.9 + - - +
49E ILE 4.7 3.0 + - - +
51E PHE 5.6 0.5 - - - +
52E ASN* 4.4 8.9 + - - +
995Q ILE* 1.3 77.7 - - - +
997Q ILE* 1.3 82.8 + - - +
999Q TYR* 4.5 7.7 + - - -
1008Q PHE* 3.3 5.7 - - - +
1009Q ARG* 2.8 59.6 + - - +
1031Q ILE* 4.3 5.2 - - - -
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Residues in contact with ILE 997 (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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44E THR* 3.3 36.3 - - + +
45E THR* 3.9 11.9 - - - -
46E ILE* 4.2 10.1 - - + +
52E ASN* 5.2 0.2 - - - +
996Q ASP* 1.3 84.0 + - - +
998Q SER* 1.3 70.5 + - - +
999Q TYR* 3.4 44.1 + - + +
1006Q ASN 6.1 0.7 - - - +
1007Q VAL 3.7 11.0 - - - +
1008Q PHE* 4.5 1.1 - - - +
1009Q ARG* 4.1 8.7 + - - -
1027Q MET* 3.7 32.1 - - + -
1028Q LEU* 4.4 0.2 - - + -
1031Q ILE* 3.8 11.9 - - + -
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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