Contacts of the strand formed by residues 289 - 294 (chain A) in PDB entry 2ZL6
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 289 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A LEU 5.1 1.1 - - - -
285A SER* 2.8 30.6 + - - +
286A HIS 3.9 3.1 - - - +
287A VAL 3.7 9.4 - - - +
288A ALA* 1.3 82.9 - - - +
290A ILE* 1.3 70.4 + - - +
304A LEU* 3.8 24.2 - - + +
318A ILE 4.8 0.7 - - - +
319A GLY 3.2 4.7 + - - +
320A PHE* 3.4 19.2 + - - -
370A VAL* 4.5 4.3 - - + -
371A GLY 3.0 15.3 - - - +
372A VAL* 3.9 21.5 - - + -
520A ACT 2.7 37.7 + - - +
247B PRO* 3.1 21.7 + - - -
248B LEU* 5.0 0.2 - - - +
249B PRO* 4.4 0.2 - - - +
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Residues in contact with ILE 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A LYS* 1.3 80.1 - - - +
291A ARG* 1.3 64.5 + - - +
292A GLY 5.5 0.4 - - - +
299A ILE* 5.1 3.4 - - + -
301A LEU* 4.5 7.6 - - + -
304A LEU* 3.6 5.4 - - - -
320A PHE* 3.6 32.3 - - + -
321A PRO* 3.7 12.1 - - + -
330A ILE* 4.2 15.7 - - + -
332A MET* 3.9 14.8 - - + -
343A TYR* 3.8 35.4 - - + -
359A ILE* 4.4 8.7 - - + -
369A TYR 5.5 0.4 - - - +
370A VAL* 3.4 7.6 - - - +
371A GLY* 2.8 44.9 + - - +
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Residues in contact with ARG 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A ILE* 1.3 76.0 - - - +
292A GLY* 1.3 61.0 + - - +
299A ILE* 5.2 0.2 - - - -
301A LEU* 3.4 12.1 - - - +
302A THR* 3.0 42.6 + - - +
303A GLU 3.6 14.8 - - - +
304A LEU* 2.9 32.2 + - + +
305A ASP* 3.8 5.7 + - - +
306A GLY* 3.8 16.1 - - - +
335A PHE* 3.9 28.1 - - - -
368A ASN* 2.9 33.1 + - - +
369A TYR 3.3 7.6 - - - -
370A VAL* 3.0 27.5 - - - +
424B LYS* 4.7 8.7 - - - +
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Residues in contact with GLY 292 (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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290A ILE* 5.5 0.6 - - - +
291A ARG* 1.3 78.6 - - - +
293A THR* 1.3 63.7 - - - -
294A SER 4.2 0.5 + - - -
299A ILE* 3.9 15.7 - - - +
300A ASN 3.1 13.9 - - - -
302A THR* 4.3 4.9 - - - -
332A MET* 6.4 0.2 - - - +
367A GLY 3.9 0.2 - - - +
368A ASN* 3.3 6.0 + - - -
369A TYR* 2.9 35.6 + - - +
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Residues in contact with THR 293 (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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292A GLY* 1.3 70.9 - - - -
294A SER* 1.3 70.8 + - - +
295A ASN* 3.9 0.8 + - + +
298A VAL 3.7 0.9 - - - +
299A ILE* 3.4 1.9 - - - -
300A ASN* 2.9 39.4 + - - +
302A THR* 5.9 1.2 - - - +
367A GLY* 3.2 16.2 - - - +
368A ASN* 3.0 22.8 + - + +
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Residues in contact with SER 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A GLY 4.1 1.0 + - - -
293A THR* 1.3 80.1 - - - +
295A ASN* 1.3 57.6 + - - +
296A GLY* 2.8 12.0 + - - -
298A VAL 3.3 6.1 - - - -
299A ILE* 3.9 16.2 - - - +
361A ALA* 3.7 6.9 - - - +
364A ILE* 2.7 29.8 + - - -
365A GLY 3.3 18.6 - - - -
366A SER* 3.2 4.7 - - - -
367A GLY 2.8 27.7 + - - -
369A TYR* 4.1 2.1 - - - -
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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