Contacts of the strand formed by residues 320 - 326 (chain E) in PDB entry 3NVQ
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 ARG 320 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307E PHE 3.6 1.4 - - - +
308E LEU* 3.3 8.4 - - - +
309E LEU* 2.9 46.0 + - + +
311E ASP* 5.3 8.9 + - - +
318E ASP 3.3 9.8 + - - +
319E THR* 1.3 73.6 - - - +
321E VAL* 1.3 61.8 + - - +
322E TYR* 2.8 38.4 + - + -
336E VAL* 3.7 8.0 - - + +
337E TYR 3.4 1.8 - - - -
394E MET* 3.6 38.7 - - - +
415E ARG* 5.6 3.1 - - - +
425E HIS* 3.4 29.4 + - - -
441E GLU* 2.6 30.5 + - - -
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Residues in contact with VAL 321 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243E PHE* 3.7 21.1 - - + -
289E LEU* 6.3 0.2 - - + -
306E VAL* 3.7 28.7 - - + -
308E LEU* 3.5 21.5 - - + -
320E ARG* 1.3 71.8 - - - +
322E TYR* 1.3 60.8 + - - +
336E VAL* 3.3 2.9 - - - -
337E TYR* 2.5 64.7 + - + +
339E LEU* 3.6 25.6 - - + -
342E ILE* 4.0 13.7 - - + -
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Residues in contact with TYR 322 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306E VAL* 3.2 8.3 - - - +
307E PHE* 3.0 46.8 + + + +
309E LEU* 3.8 18.2 - - + -
320E ARG* 2.8 52.7 + - + -
321E VAL* 1.3 75.7 - - - +
323E GLY* 1.3 59.7 + - - +
334E VAL* 4.3 10.5 - - + -
335E CYS 3.4 4.5 - - - -
336E VAL* 3.6 27.8 - - + -
401E LEU* 3.8 9.0 - - + -
411E VAL* 4.3 8.7 - - + +
413E VAL* 3.7 34.5 - - + -
425E HIS* 3.5 7.4 - - - -
427E LEU* 4.4 3.6 - - + -
441E GLU* 2.9 20.5 + - - -
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Residues in contact with GLY 323 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303E LEU* 3.9 5.6 - - - -
305E ASP 3.4 7.6 - - - -
306E VAL* 4.6 2.5 - - - -
321E VAL* 3.9 1.2 + - - -
322E TYR* 1.3 75.0 - - - +
324E VAL* 1.3 63.2 + - - -
325E PHE* 3.3 20.6 - - - -
334E VAL* 3.3 7.4 - - - +
335E CYS 2.9 33.9 + - - -
337E TYR* 5.0 2.8 - - - -
411E VAL* 5.1 0.2 - - - -
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Residues in contact with VAL 324 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303E LEU* 3.6 2.6 - - - +
304E GLN* 2.7 36.3 + - + +
305E ASP* 3.1 14.5 + - + +
323E GLY* 1.3 72.7 - - - -
325E PHE* 1.3 55.5 + - - +
332E SER* 4.4 5.6 - - - -
333E ALA 3.5 8.7 - - - +
334E VAL* 4.5 5.4 - - + -
408E TYR* 3.5 42.8 - - + +
409E GLN 4.9 0.2 - - - +
410E LYS 4.2 3.6 - - - -
411E VAL* 3.3 44.0 - - + +
429E LEU* 4.0 10.8 - - + -
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Residues in contact with PHE 325 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260E SER* 4.1 15.0 - - - -
289E LEU* 4.3 16.4 - - + -
291E CYS* 3.6 21.3 - - + -
300E PHE* 3.4 35.9 - - + +
301E ASN 4.5 0.7 - - - -
302E ARG 3.2 5.2 - - - +
303E LEU* 3.5 36.1 - - + -
304E GLN* 4.7 1.6 - - - -
323E GLY* 3.3 30.3 - - - -
324E VAL* 1.3 75.7 - - - +
326E SER* 1.3 61.1 + - - +
332E SER* 3.0 7.2 - - - -
333E ALA 2.9 34.3 + - - +
335E CYS* 4.1 5.2 - - + -
337E TYR* 3.3 30.7 - + - -
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Residues in contact with SER 326 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300E PHE* 3.5 3.5 - - - -
301E ASN 3.3 8.0 + - - -
302E ARG* 2.7 73.9 + - - +
304E GLN* 3.0 14.6 + - - -
325E PHE* 1.3 75.5 - - - +
327E ASN* 1.3 62.9 + - - +
330E ASN* 4.5 0.4 - - - -
331E TYR 3.0 14.1 - - - -
332E SER* 4.7 2.9 - - - -
407E HIS* 4.1 13.5 - - - -
408E TYR 5.2 0.4 - - - -
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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