Contacts of the strand formed by residues 359 - 364 (chain A) in PDB entry 1P22
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 MET 359 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355A PHE 2.3 29.6 - - - +
356A ASN 2.9 4.5 - - - +
357A ASN* 3.3 3.3 - - + -
358A GLY* 1.3 80.1 - - - +
360A MET* 1.3 52.6 + - - +
361A VAL* 4.8 1.1 - - - -
371A VAL* 4.3 8.7 - - - -
372A TRP 3.1 15.7 - - - +
373A ASP* 3.9 1.8 - - + -
374A MET* 4.1 3.4 - - - +
383A ARG* 3.2 48.2 - - - +
398A PHE* 2.9 40.8 - - + -
403A ILE* 5.0 0.9 - - - -
417A THR* 3.9 17.5 - - + +
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Residues in contact with MET 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A ILE* 3.4 35.0 - - + -
329A VAL* 4.9 13.0 - - - -
343A LEU* 5.8 1.6 - - - -
353A LEU* 3.5 31.0 - - + -
354A ARG 3.8 4.9 - - - +
355A PHE* 3.7 18.4 - - + -
359A MET* 1.3 75.3 - - - +
361A VAL* 1.3 72.3 + - - +
362A THR* 4.5 3.4 - - - -
371A VAL* 3.6 4.5 - - - +
372A TRP* 2.7 54.7 + - + +
374A MET* 3.6 32.4 - - + -
380A ILE* 6.0 0.2 - - - -
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Residues in contact with VAL 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353A LEU* 3.4 4.5 - - - +
354A ARG* 2.9 35.8 + - + +
359A MET* 4.8 0.7 - - - -
360A MET* 1.3 81.0 - - - +
362A THR* 1.3 65.1 - - - +
369A ILE* 3.7 14.6 - - + -
370A ALA 3.6 3.8 - - - +
371A VAL* 4.3 5.6 - - + -
396A VAL* 3.5 32.5 - - + -
397A ASP 5.4 0.9 - - - +
398A PHE* 3.6 45.8 - - + -
403A ILE* 3.9 19.5 - - + -
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Residues in contact with THR 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A VAL* 3.7 13.1 - - + +
346A HIS* 3.2 21.3 + - + +
350A VAL* 3.4 20.6 - - - +
352A HIS 3.6 6.4 + - - -
353A LEU* 4.2 5.0 - - - +
360A MET* 4.5 4.3 - - - -
361A VAL* 1.3 77.8 - - - +
363A CYS* 1.3 63.1 + - - +
369A ILE* 3.1 7.6 - - - +
370A ALA* 2.7 37.1 + - + +
372A TRP* 2.9 34.1 - - + +
396A VAL* 4.4 0.9 - - - -
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Residues in contact with CYS 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346A HIS* 4.1 4.0 + - - -
350A VAL* 3.4 7.6 - - - +
351A LEU 3.1 19.8 + - - -
352A HIS* 3.0 29.5 + - - +
362A THR* 1.3 78.4 + - - +
364A SER* 1.3 63.5 + - - +
368A SER 3.3 14.8 - - - +
369A ILE* 3.7 7.0 - - + -
393A VAL* 3.5 34.8 - - + -
395A VAL 4.0 0.4 - - - -
396A VAL* 3.4 28.7 - - + -
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Residues in contact with SER 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346A HIS* 3.4 18.1 + - - -
348A GLU 2.7 26.6 + - - -
349A ALA 3.3 9.0 - - - -
350A VAL* 4.2 0.9 - - - -
351A LEU* 3.9 9.0 - - - +
363A CYS* 1.3 80.1 - - - +
365A LYS* 1.3 69.5 + - - +
366A ASP* 2.9 26.2 + - - -
367A ARG* 3.0 13.0 + - - -
368A SER 3.2 5.1 + - - -
393A VAL 3.2 17.3 + - - -
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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