Contacts of the strand formed by residues 307 - 311 (chain B) in PDB entry 1NZX
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 307 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B LYS* 2.9 37.2 + - + +
273B SER 3.3 6.7 + - - +
274B PRO* 3.2 18.8 - - + +
275B ASN 2.8 25.2 + - - -
305B GLY 3.2 1.7 - - - -
306B SER* 1.3 82.8 - - - +
308B THR* 1.3 60.4 + - - +
309B PHE* 3.4 24.0 + - + -
391B ASP* 5.5 3.7 + - - +
396B ALA* 3.3 31.8 + - - +
406B GLN* 5.4 0.2 - - + -
408B LEU* 4.0 16.2 - - + -
419B ARG 3.0 27.1 + - - -
420B ALA* 3.0 23.8 + - - +
422B ASN 4.2 6.1 + - - -
423B SER* 3.6 19.7 + - - -
425B TYR 5.6 0.4 + - - -
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Residues in contact with THR 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B ASN* 3.5 15.7 + - - +
277B ILE* 4.3 3.1 - - + -
290B ALA* 4.3 12.1 + - + +
305B GLY 3.7 13.0 + - - -
307B ARG* 1.3 68.5 - - - +
309B PHE* 1.3 56.9 + - - +
310B VAL* 3.7 19.1 + - + +
318B PHE* 3.9 21.3 - - + -
405B MET* 3.7 18.2 - - + +
406B GLN 2.9 19.3 + - - -
407B ILE* 3.4 7.8 - - + -
408B LEU* 2.8 32.9 + - - +
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Residues in contact with PHE 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B PRO* 3.9 24.9 - - + -
275B ASN 2.8 12.0 + - - +
276B ILE* 4.1 7.0 - - + -
277B ILE* 2.8 31.0 + - - +
307B ARG* 3.4 38.3 + - + -
308B THR* 1.3 71.8 - - - +
310B VAL* 1.3 61.1 + - - +
391B ASP* 4.1 7.6 - - - -
408B LEU* 3.4 20.9 - - + -
410B PHE* 3.7 12.6 - + + -
416B VAL* 3.6 28.9 - - + -
419B ARG* 3.6 52.7 - - + -
420B ALA* 4.2 5.4 - - + -
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Residues in contact with VAL 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B ILE* 3.8 6.3 - - + -
308B THR* 3.9 7.4 - - + +
309B PHE* 1.3 78.6 - - - +
311B GLN* 1.3 68.2 + - - +
312B GLU 3.5 0.2 + - - -
314B ILE* 3.8 15.5 - - + -
315B TYR* 3.8 21.8 - - + -
318B PHE* 3.7 53.4 - - + -
407B ILE* 3.8 19.3 - - + -
408B LEU 2.8 11.3 + - - +
409B LYS* 3.3 8.5 - - - +
410B PHE* 3.1 21.5 + - - -
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Residues in contact with GLN 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B ILE 3.2 4.4 + - - +
278B MET* 5.2 3.1 - - + -
279B SER* 3.1 47.5 + - - +
310B VAL* 1.3 73.3 - - - +
312B GLU* 1.3 74.7 + - - +
313B ASP* 2.8 41.2 + - - +
314B ILE* 3.1 8.7 + - - +
315B TYR 3.0 16.6 + - - -
410B PHE* 3.1 29.3 - - + +
411B LYS* 3.6 27.2 + - - +
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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