Contacts of the strand formed by residues 360 - 363 (chain B) in PDB entry 2INU
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 VAL 360 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320B LEU* 3.4 27.4 - - + +
331B ILE* 5.0 2.5 - - + -
336B ILE* 4.0 11.4 - - + -
358B GLY 4.2 2.1 - - - -
359B VAL* 1.3 81.9 - - + +
361B HIS* 1.3 60.5 + - - +
362B ILE* 3.8 26.9 - - + -
369B ILE* 4.8 11.0 - - + -
374B PHE* 3.5 28.9 - - + -
392B GLN 2.9 8.6 + - - +
393B ILE* 3.6 13.9 - - + +
394B LEU* 2.8 30.3 + - - +
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Residues in contact with HIS 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320B LEU 2.9 12.6 + - - +
321B ARG* 3.5 3.2 - - + -
322B LEU 2.8 29.1 + - - -
323B LEU* 3.6 27.5 - - + +
357B TYR* 3.2 66.1 - + + +
358B GLY 4.6 0.9 - - - +
359B VAL 4.1 0.2 - - - -
360B VAL* 1.3 72.4 - - - +
362B ILE* 1.3 63.4 + - - +
363B ALA* 4.4 7.6 - - + -
394B LEU* 3.6 15.3 - - + +
396B ALA* 3.6 26.8 - - + +
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Residues in contact with ILE 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320B LEU* 5.0 0.7 - - + -
322B LEU* 3.8 16.4 - - + -
331B ILE* 3.7 29.8 - - + -
360B VAL* 3.8 20.4 - - + -
361B HIS* 1.3 81.9 + - - +
363B ALA* 1.3 61.9 + - - +
364B GLY 4.0 2.2 - - - +
367B ASN* 3.7 30.1 - - + +
369B ILE* 4.1 8.5 - - + -
393B ILE* 5.0 0.4 - - + -
394B LEU 2.8 9.0 + - - +
395B ILE* 3.5 27.7 - - + -
396B ALA* 2.7 32.6 + - - -
397B GLY 3.6 2.8 + - - +
401B ASN* 4.1 11.0 - - - +
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Residues in contact with ALA 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322B LEU 2.7 20.7 + - - +
323B LEU* 4.4 8.5 - - + -
324B ASN 4.6 4.5 - - - +
325B GLY* 3.3 10.2 + - - +
326B CYS* 3.1 17.8 + - - +
361B HIS* 4.4 7.2 - - + -
362B ILE* 1.3 77.0 - - - +
364B GLY* 1.3 57.9 + - - +
396B ALA* 4.2 13.0 - - + -
397B GLY* 3.7 9.4 - - - +
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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