Contacts of the strand formed by residues 336 - 343 (chain A) in PDB entry 5ZE3
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 GLU 336 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328A LEU* 3.6 12.7 - - - +
330A GLY 3.5 11.4 - - - +
331A GLY* 3.9 2.5 - - - +
332A ALA* 3.5 20.5 + - - +
333A TYR* 3.1 43.2 + - + +
334A ILE 4.7 0.2 - - - +
335A GLY* 1.3 79.9 + - - +
337A GLY* 1.3 61.4 + - - +
381A LEU* 3.8 22.7 - - + +
422A VAL 3.3 7.0 - - - +
423A ARG* 3.6 39.0 + - + +
424A CYS 6.0 0.2 - - - +
608A GLN* 5.8 0.3 + - - -
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Residues in contact with GLY 337 (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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328A LEU* 4.1 11.2 - - - +
329A ARG 3.4 11.0 - - - -
330A GLY 3.8 3.8 - - - -
336A GLU* 1.3 76.7 - - - +
338A ARG* 1.3 65.4 + - - -
339A VAL 3.5 0.2 + - - -
381A LEU* 3.7 17.7 - - - -
421A GLY* 3.1 1.2 - - - -
422A VAL* 2.8 33.5 + - - -
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Residues in contact with ARG 338 (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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327A ARG 3.3 0.5 - - - +
328A LEU* 3.1 22.8 - - - -
329A ARG* 2.8 35.0 + - - +
330A GLY* 4.6 2.6 - - - +
337A GLY* 1.3 71.1 - - - -
339A VAL* 1.3 74.2 + - - +
340A GLU* 2.9 30.5 + - + +
349A THR* 4.0 5.1 - - + +
381A LEU* 4.2 11.0 + - + +
382A GLY* 3.3 31.6 + - - +
383A GLN 3.1 23.1 + - - -
384A GLY* 3.5 18.9 - - - +
419A ASP* 4.0 13.5 - - + +
420A ALA 3.5 14.1 - - - +
421A GLY* 3.9 1.6 - - - -
549A ASP* 4.6 11.9 + - - -
724A ASP* 5.0 2.4 + - - -
727A ASN* 5.4 4.0 - - - +
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Residues in contact with VAL 339 (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 VAL* 3.9 20.0 - - + -
327A ARG 3.7 3.4 - - - -
328A LEU* 4.1 11.0 - - + -
337A GLY 3.5 0.4 + - - -
338A ARG* 1.3 77.9 - - - +
340A GLU* 1.3 70.9 + - - +
341A VAL* 4.5 2.9 - - + -
349A THR* 3.8 12.0 - - - -
350A VAL* 3.6 29.2 + - + -
355A TRP* 4.2 7.0 - - + -
363A VAL* 3.9 17.7 - - + -
402A ILE* 5.1 4.5 - - + -
420A ALA 3.0 13.5 + - - +
421A GLY* 4.2 5.6 - - - -
422A VAL* 3.7 30.1 - - + -
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Residues in contact with GLU 340 (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 VAL* 3.1 6.4 - - - +
327A ARG* 2.9 75.1 + - + +
329A ARG* 3.5 13.7 - - - +
338A ARG* 2.9 41.8 + - + +
339A VAL* 1.3 78.8 - - - +
341A VAL* 1.3 62.5 + - - +
347A TRP* 3.4 9.9 - - + -
348A GLY* 3.3 11.4 - - - +
349A THR* 4.0 15.5 - - + +
350A VAL* 5.1 0.2 - - - -
384A GLY* 4.6 2.3 - - - -
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Residues in contact with VAL 341 (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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325A LEU 3.2 10.8 - - - +
326A VAL* 3.9 5.4 - - + -
339A VAL* 4.5 7.6 - - + -
340A GLU* 1.3 79.3 - - - +
342A LEU* 1.3 65.6 + - - +
343A LYS* 4.1 11.7 - - + +
347A TRP* 3.3 6.9 - - - -
348A GLY 2.8 31.1 + - - +
350A VAL* 4.7 3.1 - - + -
389A HIS* 3.4 11.7 - - + -
390A LEU* 4.0 23.8 - - + -
402A ILE* 3.8 28.9 - - + -
403A ILE* 3.5 18.8 - - + -
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Residues in contact with LEU 342 (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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323A GLN* 3.1 31.9 - - - +
324A PRO 3.7 3.1 - - - +
325A LEU* 2.9 34.5 + - + +
341A VAL* 1.3 71.3 - - - +
343A LYS* 1.3 59.5 + - - +
345A GLY* 3.6 12.3 - - - +
346A GLU 3.3 37.5 - - - +
347A TRP* 3.5 26.1 - - + +
403A ILE* 3.5 16.6 - - - +
753A SER* 3.8 17.5 - - - +
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Residues in contact with LYS 343 (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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341A VAL* 3.6 18.5 + - + -
342A LEU* 1.3 74.1 - - - +
344A ASN* 1.3 79.7 + - - +
345A GLY 3.2 1.3 - - - -
346A GLU* 2.9 21.2 + - - +
389A HIS* 3.4 33.5 + - + +
390A LEU* 3.8 16.1 - - + +
403A ILE* 4.1 23.1 - - + +
407A PHE* 3.5 31.8 - - - -
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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