Contacts of the strand formed by residues 300 - 305 (chain B) in PDB entry 1NSC
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 PRO 300 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269B ARG* 3.9 13.7 - - - +
272B HIS 3.5 22.9 - - - +
273B THR* 4.0 17.5 - - + +
288B CYS 3.7 0.5 - - - +
289B ALA* 3.7 1.2 - - - -
290B CYS* 2.9 42.0 + - + +
291B ARG 4.3 2.5 - - - +
292B ASP* 3.9 17.5 - - + +
298B LYS 3.6 8.1 - - - +
299B ARG* 1.4 82.0 - - - +
301B PHE* 1.3 59.7 + - - +
302B VAL 4.1 0.4 - - - -
313B ILE* 3.9 17.9 - - + -
314B ARG 4.1 4.5 - - - +
315B LEU* 4.0 8.7 - - + -
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Residues in contact with PHE 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287B GLU* 3.5 42.6 - - + -
288B CYS 3.2 10.5 - - - -
289B ALA* 4.4 3.1 - - - -
299B ARG 3.3 0.2 + - - -
300B PRO* 1.3 73.5 - - - +
302B VAL* 1.3 69.9 + - - +
303B LYS* 4.1 9.9 - - + -
313B ILE* 3.5 3.5 - - - +
314B ARG 2.9 28.5 + - - +
316B MET* 3.6 33.7 - - + -
351B PHE* 3.7 22.9 - + - -
362B ARG* 4.1 0.9 - - - -
364B TYR* 3.7 15.3 - + - -
386B PRO* 3.9 22.9 - - + -
387B TRP* 2.9 40.8 + + + +
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Residues in contact with VAL 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B PHE* 3.9 27.1 - - + -
273B THR* 4.5 1.3 - - + -
276B CYS* 4.2 5.4 - - - -
286B ILE 5.2 0.2 - - - +
287B GLU* 3.2 9.2 - - - +
288B CYS* 3.0 37.9 + - + -
290B CYS* 3.8 25.4 - - - -
301B PHE* 1.3 76.2 - - - +
303B LYS* 1.3 75.8 + - - +
304B LEU* 4.0 6.3 - - + +
311B ALA* 4.2 10.3 - - + -
312B GLU 3.5 8.7 - - - +
313B ILE* 3.8 26.5 - - + -
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Residues in contact with LYS 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B THR* 4.6 9.9 - - + -
286B ILE 3.7 4.3 - - - -
287B GLU* 4.6 11.9 - - + +
301B PHE* 4.1 17.3 - - + -
302B VAL* 1.3 77.3 - - - +
304B LEU* 1.3 60.4 + - - +
305B ASN 4.0 1.0 + - - -
310B THR 4.1 0.2 - - - +
311B ALA* 3.4 1.9 - - - -
312B GLU* 2.9 30.7 + - + +
362B ARG* 5.8 0.7 - - - +
385B ASP* 2.6 43.8 + - - -
386B PRO* 4.6 4.7 - - - +
387B TRP* 3.6 46.4 - - + +
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Residues in contact with LEU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B TYR* 4.0 38.1 - - + -
252B PHE* 3.6 43.3 - - + -
264B ILE* 4.4 9.0 - - + -
285B THR* 3.3 6.5 - - - +
286B ILE* 2.8 51.8 + - + +
302B VAL* 4.4 5.2 - - + -
303B LYS* 1.3 72.4 - - - +
305B ASN* 1.3 79.1 + - - +
306B VAL* 3.4 7.5 + - + +
309B ASP* 4.7 0.4 - - - +
310B THR 3.5 10.3 - - - +
311B ALA* 4.1 11.7 - - + +
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Residues in contact with ASN 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284B LYS* 3.6 34.9 - - - +
285B THR* 4.8 3.1 + - - +
303B LYS 4.0 1.6 + - - -
304B LEU* 1.3 72.7 - - - +
306B VAL* 1.3 56.7 + - - +
307B GLU* 2.8 35.2 + - - +
308B THR* 3.0 27.0 + - - +
309B ASP* 2.8 31.4 + - - -
310B THR* 2.8 17.8 + - - +
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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