Contacts of the strand formed by residues 486 - 493 (chain A) in PDB entry 1Z3S
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 ALA 486 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328A ARG* 3.2 15.9 - - - +
329A GLU* 3.8 10.1 - - + -
374A HIS 4.6 0.4 - - - -
375A LEU* 3.7 0.7 - - - -
376A LYS* 3.0 63.8 + - + +
484A LEU* 3.6 0.7 - - - +
485A LYS* 1.3 85.9 - - + +
487A THR* 1.3 68.9 + - - +
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Residues in contact with THR 487 (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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326A GLN* 2.8 20.4 + - - -
327A ARG* 3.4 2.4 - - - +
328A ARG* 2.8 48.4 + - + +
374A HIS 3.3 8.1 - - - -
375A LEU* 3.9 19.7 - - + -
376A LYS* 6.2 0.7 - - - +
455A LEU* 4.1 11.3 + - + -
472A ILE* 3.5 30.3 - - + -
484A LEU* 4.0 6.3 - - + -
486A ALA* 1.3 80.8 - - - +
488A THR* 1.3 66.9 + - - +
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Residues in contact with THR 488 (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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324A ILE* 3.3 18.2 - - - +
326A GLN* 3.4 8.7 + - - +
327A ARG* 4.2 13.3 + - - -
372A LYS 3.6 2.3 - - - +
373A ILE* 3.4 4.7 - - - +
374A HIS* 2.9 63.6 + - + +
376A LYS* 5.4 6.7 - - - +
487A THR* 1.3 79.6 - - - +
489A MET* 1.3 63.0 + - - +
490A MET* 3.2 20.6 - - + +
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Residues in contact with MET 489 (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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324A ILE* 3.5 5.2 - - - +
325A ILE* 2.7 50.8 + - + -
326A GLN* 2.9 42.6 + - + +
354A TRP* 4.4 9.6 - - - -
371A LEU* 4.5 15.5 - - + -
372A LYS 3.7 4.0 - - - -
373A ILE* 4.2 21.1 - - + +
416A ILE* 5.4 2.5 - - + -
445A TRP* 5.0 3.1 - - + +
446A TRP* 3.7 32.8 - - + -
455A LEU* 4.1 24.5 - - + -
488A THR* 1.3 75.2 - - - +
490A MET* 1.3 55.9 + - - +
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Residues in contact with MET 490 (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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314A ASP* 4.6 11.4 - - - +
317A ALA* 5.4 3.4 - - + -
322A TRP* 3.7 43.1 - - + -
323A THR 3.2 10.3 - - - +
324A ILE* 3.5 20.0 - - + -
325A ILE 4.4 0.4 - - - +
371A LEU* 3.6 3.6 - - - +
372A LYS* 2.8 56.0 + - + +
374A HIS* 4.2 9.9 - - + -
488A THR* 3.2 46.9 - - + +
489A MET* 1.3 76.6 - - - +
491A ILE* 1.3 64.5 + - - +
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Residues in contact with ILE 491 (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 GLY 4.2 0.2 - - - +
322A TRP* 3.6 3.1 - - - -
323A THR* 2.9 47.6 + - + +
325A ILE* 4.2 19.7 - - + -
360A VAL* 4.8 6.7 - - + -
363A LEU* 4.3 15.3 - - + -
364A THR* 4.2 13.2 - - + -
369A TYR* 3.6 28.9 - - + -
370A VAL 3.1 12.1 - - - +
371A LEU* 3.7 21.3 - - + -
390A PHE* 3.8 18.6 - - + -
490A MET* 1.3 79.2 - - - +
492A ARG* 1.3 65.7 + - - +
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Residues in contact with ARG 492 (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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285A ALA* 5.0 0.7 - - + -
318A GLY 2.8 29.1 + - - -
319A GLY* 3.8 5.0 - - - -
320A GLY 3.0 21.9 + - - +
321A GLY 4.0 13.9 - - - +
322A TRP* 2.9 47.9 - - + +
323A THR* 5.9 0.2 - - - -
369A TYR* 3.6 6.7 - - - -
370A VAL* 2.7 31.0 + - - +
491A ILE* 1.3 81.1 - - - +
493A PRO* 1.3 85.9 - - + +
495A ASP* 3.1 30.4 + - - +
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Residues in contact with PRO 493 (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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283A ASP* 4.0 0.7 - - - +
285A ALA* 3.6 27.8 - - + -
367A GLN* 3.6 35.0 - - + +
368A ARG 3.5 17.3 - - - +
369A TYR* 3.7 15.0 - - + -
370A VAL* 4.9 6.1 - - - +
492A ARG* 1.3 108.8 - - + +
494A ALA* 1.3 62.5 + - - +
495A ASP* 3.0 16.4 + - + -
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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