Contacts of the strand formed by residues 453 - 457 (chain T) in PDB entry 2P8Z
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 ILE 453 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13T MET* 5.2 3.8 - - - +
21T ASN* 4.2 23.8 - - - +
74T ALA* 5.5 6.5 - - + -
101T ASN* 5.4 10.2 + - + +
103T ILE* 4.3 17.7 - - + -
121T VAL* 3.8 28.3 - - + +
397T PHE* 3.4 29.6 - - + -
398T GLY 3.4 9.6 - - - +
399T ARG* 4.1 14.4 - - - -
436T LEU* 5.3 1.9 - - - +
437T MET* 5.4 6.7 - - + +
448T CYS* 4.3 0.3 - - - -
452T ASN* 1.3 83.6 - - - +
454T ILE* 1.3 76.5 + - - +
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Residues in contact with ILE 454 (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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380T LEU* 4.4 15.7 - - + -
396T ALA 4.0 0.2 - - - +
397T PHE* 3.8 3.0 - - - -
398T GLY 2.9 39.1 + - - +
400T VAL* 4.0 22.9 - - + -
405T VAL* 4.6 3.6 - - + -
434T VAL* 3.5 28.9 - - + -
435T VAL 3.1 24.2 - - - +
436T LEU* 3.9 18.8 - - + -
437T MET* 4.1 9.2 - - - +
445T ILE* 4.5 2.7 - - + -
448T CYS* 4.0 19.1 - - + -
453T ILE* 1.3 85.4 - - - +
455T GLY* 1.3 65.8 + - - +
456T LEU* 4.6 5.2 - - + +
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Residues in contact with GLY 455 (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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396T ALA 3.2 9.6 - - - -
434T VAL* 3.7 2.9 - - - -
435T VAL* 2.8 48.9 + - - +
437T MET* 3.7 21.7 - - - +
454T ILE* 1.3 75.8 - - - +
456T LEU* 1.3 63.3 + - - +
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Residues in contact with LEU 456 (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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380T LEU* 3.5 26.5 - - + -
382T VAL* 4.9 0.7 - - + -
395T TYR* 3.6 6.0 - - - +
396T ALA* 2.7 48.7 + - + +
405T VAL* 3.9 20.9 - - + -
431T ILE* 3.9 22.2 - - + -
433T ARG 3.8 1.1 - - - -
434T VAL* 4.1 9.2 - - + -
435T VAL* 5.2 0.2 - - - -
454T ILE* 4.6 6.5 - - + +
455T GLY* 1.3 80.2 - - - +
457T VAL* 1.3 60.2 + - - +
458T GLY 4.1 0.9 + - - -
459T ILE* 3.9 17.9 + - + +
469T LEU* 3.4 34.3 - - + -
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Residues in contact with VAL 457 (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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393T ARG* 5.4 2.9 - - - +
395T TYR* 4.1 35.0 - - + +
431T ILE* 4.2 4.2 - - - +
432T GLN* 3.4 39.2 + - + +
433T ARG* 2.9 42.7 + - + +
435T VAL* 4.0 16.2 - - + -
456T LEU* 1.3 75.2 - - - +
458T GLY* 1.3 64.0 + - - +
459T ILE* 3.5 0.7 - - - -
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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