Contacts of the strand formed by residues 314 - 320 (chain A) in PDB entry 3ZDT
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 GLY 314 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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305A SER 3.8 6.3 - - - -
306A ASN* 4.4 0.4 - - - -
312A ARG 3.9 0.6 + - - -
313A LYS* 1.3 71.9 - - - +
315A MET* 1.3 65.2 + - - -
316A LEU* 5.0 0.5 - - - +
329A VAL 3.6 0.3 - - - +
330A THR* 3.3 5.4 - - - -
331A ALA* 2.6 42.5 + - - +
333A SER 3.9 18.1 - - - -
334A LEU* 4.2 4.9 - - - -
337A ALA* 4.2 8.6 - - - +
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Residues in contact with MET 315 (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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264A SER* 6.1 2.0 - - - -
303A GLN 4.8 0.2 - - - -
304A TYR* 3.4 7.3 - - - +
305A SER* 2.7 47.3 + - - +
306A ASN 3.7 15.5 - - - +
307A SER* 3.8 15.9 - - - -
308A GLU* 4.8 4.0 - - - +
313A LYS 4.1 0.4 + - - -
314A GLY* 1.3 73.2 - - - -
316A LEU* 1.3 59.8 + - - +
317A GLN* 5.1 7.9 - - + +
328A THR* 3.2 35.4 - - + -
329A VAL 3.5 1.6 - - - -
330A THR* 3.6 29.2 - - - +
337A ALA* 4.4 2.8 - - - +
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Residues in contact with LEU 316 (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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302A ILE* 4.0 12.8 - - + -
303A GLN 3.5 7.4 - - - +
304A TYR* 3.4 23.6 - - + -
314A GLY 5.0 1.6 - - - +
315A MET* 1.3 75.9 - - - +
317A GLN* 1.3 59.2 + - - +
318A LEU* 4.5 8.5 - - + -
327A LEU 3.7 0.9 - - - +
328A THR* 3.4 1.8 - - - +
329A VAL* 2.5 65.7 + - + +
331A ALA* 6.2 0.4 - - + -
337A ALA* 4.3 9.0 - - + +
340A MET* 3.8 30.5 - - + -
341A ALA* 3.9 22.2 - - + +
344A ILE* 4.4 14.6 - - + -
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Residues in contact with GLN 317 (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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301A THR* 4.1 0.9 + - - +
302A ILE 3.9 0.2 - - - -
303A GLN* 2.8 52.8 + - + +
315A MET* 5.1 7.3 - - + +
316A LEU* 1.3 76.4 - - - +
318A LEU* 1.3 62.9 + - - +
319A LYS 4.3 0.2 - - - -
326A PRO* 3.9 26.2 - - + +
327A LEU 3.4 2.9 - - - -
328A THR* 3.3 28.8 + - + +
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Residues in contact with LEU 318 (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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280A ILE* 4.3 15.9 - - + -
299A VAL* 5.1 4.7 - - + -
301A THR 3.3 4.7 - - - +
302A ILE* 3.7 39.3 - - + -
316A LEU* 4.5 11.9 - - + +
317A GLN* 1.3 83.8 - - - +
319A LYS* 1.3 61.3 + - - +
320A ILE* 3.6 17.5 + - + +
326A PRO* 3.3 6.9 - - - +
327A LEU* 2.9 49.6 + - + +
329A VAL* 5.2 7.6 - - + -
344A ILE* 4.1 26.5 - - + -
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Residues in contact with LYS 319 (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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299A VAL* 3.6 0.9 - - - -
300A GLN* 2.6 50.2 + - + +
301A THR* 3.0 45.8 + - + +
303A GLN* 4.9 8.0 - - - +
317A GLN 4.4 0.4 + - - -
318A LEU* 1.3 71.0 - - - +
320A ILE* 1.3 59.8 + - - +
326A PRO* 4.7 15.3 - - + -
360A ILE* 4.6 10.9 - - - +
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Residues in contact with ILE 320 (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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280A ILE* 5.6 1.1 - - + -
293A LEU 5.2 1.3 - - - +
294A ALA* 3.6 25.4 - - + -
298A GLN* 3.3 33.9 - - + +
299A VAL* 4.3 14.4 - - + -
300A GLN* 4.6 2.0 - - - -
318A LEU* 3.6 16.4 + - + +
319A LYS* 1.3 79.2 - - - +
321A ALA* 1.3 70.4 + - - +
323A ALA* 3.2 34.2 + - + +
325A GLU 5.7 1.3 + - - +
326A PRO* 5.2 2.6 - - - +
327A LEU* 4.1 34.5 - - + +
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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