Contacts of the strand formed by residues 302 - 309 (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 302 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E NAG 5.5 5.8 - - - -
245E ARG* 3.9 22.9 - - - +
258E ASN* 5.7 7.9 - - + +
260E SER* 4.0 0.4 - - - -
300E PHE 3.6 0.4 - - - -
301E ASN* 1.3 86.0 - - - +
303E LEU* 1.3 60.4 + - - +
304E GLN* 2.6 40.3 + - - +
325E PHE* 3.2 2.8 - - - -
326E SER* 2.7 52.2 + - - +
327E ASN 2.8 24.5 + - - -
328E PRO* 4.9 1.8 - - - +
330E ASN* 2.7 26.6 + - - -
407E HIS* 3.6 10.3 + - - -
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Residues in contact with LEU 303 (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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225E ILE* 4.5 11.1 - - + +
243E PHE* 4.1 17.5 - - + -
244E PHE 4.7 5.8 - - - +
245E ARG* 2.7 40.5 + - + +
260E SER* 3.0 27.0 + - - +
261E ARG 4.7 0.2 - - - +
289E LEU* 4.3 17.0 - - + -
301E ASN 3.7 0.2 - - - -
302E ARG* 1.3 69.3 - - - +
304E GLN* 1.3 54.7 + - - +
305E ASP 3.7 17.5 - - - +
306E VAL* 3.9 20.9 - - + -
323E GLY* 3.9 5.4 - - - -
324E VAL 3.6 11.9 - - - +
325E PHE* 3.5 33.4 - - + -
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Residues in contact with GLN 304 (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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225E ILE* 3.9 16.0 - - - +
245E ARG* 3.8 12.9 + - - +
302E ARG* 2.6 45.5 + - - +
303E LEU* 1.3 79.3 + - - +
305E ASP* 1.3 63.3 + - - +
324E VAL* 2.7 18.6 + - + +
326E SER* 3.0 14.4 + - - +
407E HIS* 3.5 11.4 - - - -
408E TYR 3.7 17.0 - - - +
409E GLN* 3.6 23.2 + - - +
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Residues in contact with ASP 305 (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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225E ILE* 3.9 7.8 - - - +
226E LYS* 3.6 22.1 + - - -
303E LEU* 3.7 2.2 - - - +
304E GLN* 1.3 81.9 - - - +
306E VAL* 1.3 73.0 + - - +
322E TYR 3.9 0.2 - - - +
323E GLY* 3.4 4.3 - - - -
324E VAL* 3.1 26.7 + - + +
409E GLN 3.2 17.7 - - - +
410E LYS* 3.4 21.3 + - - +
411E VAL* 3.1 32.5 + - + +
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Residues in contact with VAL 306 (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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225E ILE* 4.2 6.0 - - + +
226E LYS* 3.6 35.8 - - + +
243E PHE* 4.1 29.2 - - + -
289E LEU* 6.1 0.2 - - + -
303E LEU* 3.9 28.7 - - + -
305E ASP* 1.3 88.5 + - - +
307E PHE* 1.3 70.2 + - - +
308E LEU* 4.5 5.2 - - + -
321E VAL* 3.7 28.0 - - + -
322E TYR 3.2 7.6 - - - +
323E GLY* 4.7 0.9 - - - -
411E VAL* 4.5 2.8 - - - +
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Residues in contact with PHE 307 (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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226E LYS* 6.2 0.2 - - - -
306E VAL* 1.3 76.4 - - - +
308E LEU* 1.3 83.1 + - - +
309E LEU* 4.1 11.2 - - + -
320E ARG 3.6 1.2 - - - +
321E VAL* 3.9 0.3 - - - -
322E TYR* 3.0 35.6 + + + +
411E VAL* 3.5 23.3 - - + +
412E ALA* 3.7 24.5 - - + -
413E VAL* 3.4 47.8 - - + -
470E LEU* 4.3 12.3 - - + -
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Residues in contact with LEU 308 (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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226E LYS* 6.1 2.2 - - + -
228E THR* 3.2 45.8 - - + +
243E PHE* 5.1 5.2 - - + -
306E VAL* 4.5 6.7 - - + -
307E PHE* 1.3 91.9 - - - +
309E LEU* 1.3 60.8 + - - +
310E PRO* 3.9 8.3 - - + +
319E THR* 4.5 13.9 - - + -
320E ARG 3.3 5.6 - - - +
321E VAL* 3.5 43.5 - - + -
339E LEU* 4.7 7.9 - - + -
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Residues in contact with LEU 309 (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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307E PHE* 4.1 9.9 - - + -
308E LEU* 1.3 74.9 - - - +
310E PRO* 1.4 70.2 - - + +
311E ASP* 3.7 0.5 + - - -
318E ASP 4.4 0.2 - - - +
319E THR* 3.7 1.9 - - - +
320E ARG* 2.9 39.2 + - + +
322E TYR* 3.8 27.6 - - + +
413E VAL* 4.1 24.9 - - + +
415E ARG* 3.9 36.3 + - + +
425E HIS* 3.6 31.6 - - + +
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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