Contacts of the strand formed by residues 357 - 363 (chain A) in PDB entry 1ZGA
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 LYS 357 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A ASP* 3.4 30.7 + - - -
265A TRP* 5.2 11.9 - - - +
298A ILE* 5.9 1.6 - - + -
299A ASP 4.6 3.1 - - - +
300A ILE* 3.6 30.7 - - + +
315A GLN* 5.3 0.3 - - - +
318A TYR* 4.9 8.9 + - - -
352A PRO* 3.6 5.0 - - - +
353A ILE* 2.8 39.3 + - + +
354A SER* 3.8 22.9 - - - +
356A PHE* 1.3 109.9 - - + +
358A SER* 1.3 67.6 + - - +
365A HMK 5.5 1.6 - - - -
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Residues in contact with SER 358 (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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297A ILE 3.8 0.2 - - - +
298A ILE* 3.5 2.1 - - - -
299A ASP 3.0 38.2 + - - +
301A SER* 3.5 31.4 + - - -
315A GLN* 5.0 1.4 + - - -
350A ILE* 3.7 22.7 - - - +
351A THR 3.6 4.2 + - - -
352A PRO* 4.8 1.9 - - - +
353A ILE* 3.5 12.3 - - - +
356A PHE 4.8 0.3 + - - -
357A LYS* 1.3 82.6 + - - +
359A LEU* 1.3 60.4 + - - +
360A ILE* 4.0 6.3 - - - -
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Residues in contact with LEU 359 (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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189A VAL* 4.2 22.2 - - + -
193A ASN* 4.7 8.5 - - + -
196A VAL* 4.1 24.2 - - + -
197A PHE* 5.0 7.0 - - + -
296A ILE* 3.9 26.0 - - + -
297A ILE 3.4 2.2 - - - -
298A ILE* 4.3 14.6 - - + -
349A LYS 3.6 1.0 - - - +
350A ILE* 3.5 0.9 - - - -
351A THR* 2.7 49.8 + - - +
353A ILE* 3.9 14.1 - - + -
358A SER* 1.3 73.2 - - - +
360A ILE* 1.3 63.5 + - - +
361A GLU* 3.9 21.8 - - + +
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Residues in contact with ILE 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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295A VAL 3.5 1.4 - - - +
296A ILE* 3.4 5.2 - - - -
297A ILE* 2.6 58.3 + - + +
299A ASP 5.4 2.2 - - - +
301A SER* 4.6 3.8 - - - -
336A TRP* 3.9 46.2 - - + +
340A ILE* 4.0 12.6 - - + -
348A TYR* 4.3 3.8 - - + -
349A LYS 3.4 7.6 - - - +
350A ILE* 4.2 22.9 - - + -
358A SER* 4.5 10.5 - - - +
359A LEU* 1.3 78.8 - - - +
361A GLU* 1.3 66.0 + - - +
362A VAL* 3.7 18.6 + - + +
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Residues in contact with GLU 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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195A ARG* 2.9 33.2 + - - -
196A VAL* 3.7 15.3 - - + +
294A LYS* 2.6 36.3 + - - +
295A VAL 3.8 3.1 - - - -
296A ILE* 4.9 2.5 - - + -
348A TYR* 3.0 6.8 - - - +
349A LYS* 2.7 53.2 + - + +
351A THR* 4.4 8.8 + - - -
359A LEU* 3.9 15.0 - - + -
360A ILE* 1.3 71.0 - - - +
362A VAL* 1.3 59.9 + - - +
363A TYR* 3.1 26.3 + - + +
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Residues in contact with VAL 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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279A LEU* 5.6 1.3 - - + -
294A LYS* 3.5 8.2 - - - +
295A VAL* 2.8 46.1 + - + +
297A ILE* 4.0 17.3 - - + -
340A ILE* 3.7 35.0 - - + -
345A PHE* 3.2 47.5 - - + -
347A SER 3.7 2.5 - - - -
360A ILE* 3.9 9.9 - - + +
361A GLU* 1.3 77.1 - - - +
363A TYR* 1.3 62.7 + - - +
364A PRO* 4.2 1.0 - - - +
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Residues in contact with TYR 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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195A ARG* 3.7 11.1 + - - -
291A LYS 5.1 6.5 - - - +
292A ASP 5.7 1.6 - - - -
293A GLY 4.2 6.7 - - - -
294A LYS* 3.6 26.6 + - + -
345A PHE* 3.4 6.8 - - - +
346A SER 2.7 31.9 + - - -
347A SER* 2.8 40.6 + - - +
348A TYR* 4.4 0.9 - - - -
349A LYS* 4.8 9.3 - - + +
361A GLU* 3.1 51.3 + - + -
362A VAL* 1.3 76.2 - - - +
364A PRO* 1.3 62.9 - - + +
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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