Contacts of the strand formed by residues 315 - 319 (chain A) in PDB entry 3NZI
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 ASP 315 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300A THR 5.1 1.7 - - - +
301A GLN* 3.8 35.6 - - + +
302A ARG 3.5 4.0 - - - +
303A GLY* 3.2 18.5 - - - -
313A ASP 4.0 5.1 + - - +
314A MET* 1.3 89.0 - - + +
316A TYR* 1.3 63.5 + - - +
356A PRO* 2.9 28.8 - - + +
359A LYS* 6.1 1.6 - - - -
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Residues in contact with TYR 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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248A LYS 5.5 2.4 + - - -
249A ALA* 5.9 1.7 - - - -
250A ASP* 6.1 0.9 - - - +
300A THR 3.8 2.6 - - - +
302A ARG* 2.8 40.3 + - - +
304A GLY* 3.9 23.3 - - - -
307A LEU* 3.9 19.3 - - + -
309A LEU* 3.7 19.8 - - + +
312A SER* 4.6 0.3 + - - -
314A MET* 3.5 26.2 - - + +
315A ASP* 1.3 73.4 - - - +
317A ILE* 1.3 62.4 + - - +
318A GLN 3.8 1.2 + - - -
344A THR* 4.6 1.7 - - + +
345A LEU* 4.2 19.0 - - + +
353A PHE* 3.8 26.5 - - + -
354A ALA 3.4 17.7 - - - +
355A ILE* 3.3 35.5 - - + +
356A PRO* 4.3 0.4 - - - -
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Residues in contact with ILE 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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270A SER* 4.2 11.7 - - - -
273A LEU* 3.3 33.7 - - + -
297A VAL* 4.3 8.5 - - + -
299A THR 3.7 9.2 - - - +
300A THR 3.7 13.2 - - - +
315A ASP 3.9 0.2 + - - -
316A TYR* 1.3 72.9 - - - +
318A GLN* 1.3 71.5 + - - +
319A THR* 4.1 0.9 + - - +
332A LEU* 4.5 12.8 - - + -
340A ILE* 3.1 31.9 - - + +
341A GLY* 4.9 2.9 - - - -
353A PHE* 3.3 5.8 - - - -
354A ALA* 3.0 39.1 + - + +
356A PRO* 4.3 14.4 - - + -
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Residues in contact with GLN 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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297A VAL* 3.5 6.4 - - - -
298A SER* 2.6 47.0 + - - -
299A THR* 2.9 25.7 + - + +
302A ARG* 2.7 40.7 + - + +
316A TYR 3.8 1.1 + - - +
317A ILE* 1.3 76.3 - - - +
319A THR* 1.3 59.4 + - - +
350A GLY 5.5 1.2 + - - +
351A ILE* 4.0 23.4 - - + +
352A SER 3.5 6.3 - - - +
353A PHE* 3.4 26.4 - - + -
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Residues in contact with THR 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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279A VAL* 3.6 10.3 - - - +
296A ILE 3.3 13.7 + - - -
297A VAL* 5.0 0.7 - - - -
298A SER* 3.6 4.5 - - - -
317A ILE* 5.2 0.4 - - - +
318A GLN* 1.3 77.0 - - - +
320A ASP* 1.3 59.0 + - - +
321A ALA* 2.9 32.8 + - + +
323A ILE* 5.4 2.0 - - + -
332A LEU* 4.4 27.4 - - + -
343A ASN* 5.1 4.5 - - - +
350A GLY 3.5 4.8 - - - +
351A ILE* 3.9 0.2 - - - -
352A SER* 2.9 48.2 + - - +
353A PHE* 4.8 2.2 - - - +
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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