Contacts of the strand formed by residues 300 - 305 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269A ARG* 4.0 10.8 - - - +
272A HIS 3.6 20.6 - - - +
273A THR* 4.1 16.8 - - + +
288A CYS 3.7 0.3 - - - +
289A ALA* 3.7 1.4 - - - -
290A CYS* 2.9 42.3 + - + +
291A ARG 4.3 2.0 - - - +
292A ASP* 3.8 22.0 - - + +
298A LYS 3.6 8.1 - - - +
299A ARG* 1.4 81.3 - - - +
301A PHE* 1.3 57.9 + - - +
302A VAL 4.1 0.2 - - - -
313A ILE* 4.0 17.7 - - + -
314A ARG 4.0 5.2 - - - +
315A LEU* 4.0 9.2 - - + -
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Residues in contact with PHE 301 (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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287A GLU* 3.4 47.6 - - + -
288A CYS 3.1 12.8 - - - -
289A ALA* 4.3 3.1 - - - -
300A PRO* 1.3 72.5 - - - +
302A VAL* 1.3 65.3 + - - +
303A LYS* 4.2 10.1 - - + -
313A ILE* 3.6 3.5 - - - +
314A ARG 2.9 25.0 + - - +
316A MET* 3.8 31.4 - - + -
351A PHE* 3.8 20.6 - + - -
362A ARG* 4.1 1.6 - - - -
364A TYR* 3.8 16.8 - + - -
386A PRO* 3.7 23.6 - - + -
387A TRP* 2.9 39.3 + + + +
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Residues in contact with VAL 302 (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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252A PHE* 3.9 26.9 - - + -
273A THR* 4.5 0.7 - - + -
276A CYS* 4.2 5.6 - - - -
287A GLU* 3.0 10.0 - - - +
288A CYS* 2.9 37.8 + - + -
290A CYS* 3.8 24.2 - - - -
301A PHE* 1.3 76.0 - - - +
303A LYS* 1.3 75.5 + - - +
304A LEU* 4.2 6.7 - - + +
311A ALA* 4.3 9.9 - - + -
312A GLU 3.6 8.3 - - - +
313A ILE* 3.9 25.1 - - + +
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Residues in contact with LYS 303 (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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285A THR* 4.4 10.1 - - + -
286A ILE 3.6 4.5 - - - -
287A GLU* 4.4 13.9 - - + +
301A PHE* 4.2 18.2 - - + -
302A VAL* 1.3 76.7 - - - +
304A LEU* 1.3 59.7 + - - +
305A ASN 4.1 0.9 + - - -
311A ALA* 3.4 1.4 - - - -
312A GLU* 3.1 31.0 + - + +
362A ARG* 5.9 0.2 - - - +
385A ASP* 2.7 41.0 + - - -
386A PRO* 4.7 4.6 - - - +
387A TRP* 3.7 43.3 - - + +
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Residues in contact with LEU 304 (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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236A TYR* 3.8 36.8 - - + -
252A PHE* 3.6 37.0 - - + -
264A ILE* 4.3 8.5 - - + -
285A THR* 3.3 7.6 - - - +
286A ILE* 2.8 49.9 + - + +
302A VAL* 4.3 6.1 - - + -
303A LYS* 1.3 73.5 - - - +
305A ASN* 1.3 77.3 + - - +
306A VAL* 3.5 2.8 + - + +
310A THR 3.5 16.6 - - - +
311A ALA* 3.9 14.6 - - + -
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Residues in contact with ASN 305 (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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284A LYS* 3.4 40.0 - - - +
285A THR* 4.8 2.7 - - - +
303A LYS 4.1 1.4 + - - -
304A LEU* 1.3 70.8 - - - +
306A VAL* 1.3 53.5 + - - +
307A GLU* 2.7 35.0 + - - +
308A THR* 3.0 33.6 + - - +
309A ASP* 2.7 36.0 + - - -
310A THR* 2.8 17.2 + - - +
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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