Contacts of the strand formed by residues 293 - 301 (chain A) in PDB entry 5NRO
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 293 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285A TYR* 3.7 37.5 - - + -
287A THR 3.4 10.1 - - - +
288A ALA* 4.0 11.4 - - + -
292A GLY* 1.3 87.5 - - - +
294A LYS* 1.3 66.1 + - - +
295A HIS* 4.8 7.6 + - + +
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Residues in contact with LYS 294 (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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244A PHE* 4.0 10.8 - - + -
248A GLN* 3.8 25.2 - - + +
250A ILE* 3.9 22.9 - - + -
285A TYR* 3.3 1.9 - - - -
286A ILE* 3.1 23.8 + - - +
287A THR* 2.7 26.4 + - + +
289A ASP* 3.6 28.2 + - + -
291A THR* 4.1 9.7 + - - -
292A GLY* 3.7 8.1 + - - +
293A PRO* 1.3 80.6 + - - +
295A HIS* 1.3 74.9 + - - +
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Residues in contact with HIS 295 (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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244A PHE* 3.2 17.6 - - - -
248A GLN* 3.7 14.9 + - - +
283A LEU 3.8 4.7 - - - +
284A PRO* 3.7 10.7 - - + +
285A TYR* 2.9 61.5 + + - -
286A ILE* 3.9 1.8 - - - -
293A PRO* 4.8 8.1 + - - +
294A LYS* 1.3 83.4 + - - +
296A MET* 1.3 63.3 + - - +
297A ASN* 6.2 0.7 - - + -
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Residues in contact with MET 296 (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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240A LEU* 4.5 11.0 - - - +
244A PHE* 4.0 24.0 - - + -
252A LEU* 5.2 5.2 - - - -
262A LEU* 3.5 25.6 - - + -
281A VAL* 3.5 31.4 - - + +
282A ASN* 3.5 4.5 - - - +
283A LEU* 2.9 54.7 + - + +
286A ILE* 4.1 5.8 - - + +
295A HIS* 1.3 78.4 - - - +
297A ASN* 1.3 65.4 + - - +
298A ILE* 3.6 32.3 - - + -
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Residues in contact with ASN 297 (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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280A ASP* 4.0 23.8 + - - +
281A VAL 3.3 4.5 - - - +
282A ASN* 4.0 23.8 + - - +
295A HIS* 6.2 0.7 - - + -
296A MET* 1.3 76.7 - - - +
298A ILE* 1.3 62.9 + - - +
299A LYS* 4.3 3.3 + - - +
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Residues in contact with ILE 298 (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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239A TYR* 4.5 13.2 - - + +
240A LEU* 3.8 31.4 - - + +
243A GLU* 4.1 24.2 - - + -
244A PHE* 4.8 3.6 - - + +
247A ASP* 5.8 2.7 - - - +
280A ASP* 3.4 3.9 - - - -
281A VAL* 2.9 35.0 + - + +
296A MET* 3.6 34.8 - - + -
297A ASN* 1.3 80.1 + - - +
299A LYS* 1.3 77.0 + - - +
300A VAL* 3.7 3.9 + - + +
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Residues in contact with LYS 299 (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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239A TYR* 4.9 5.2 + - - -
278A GLN* 4.0 24.0 - - - +
280A ASP* 3.3 23.1 - - - +
297A ASN* 4.3 3.7 + - - +
298A ILE* 1.3 82.1 - - - +
300A VAL* 1.3 64.9 + - - +
301A THR* 4.3 2.7 - - + +
304A LYS* 5.9 0.9 - - - +
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Residues in contact with VAL 300 (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 LEU* 4.7 19.3 - - + -
239A TYR* 4.8 5.4 - - + -
240A LEU* 4.7 7.2 - - + -
269A ALA* 5.8 0.4 - - + -
273A LEU* 3.6 20.1 - - + +
278A GLN* 3.3 3.3 - - - -
279A THR* 2.9 41.2 + - + +
281A VAL* 4.2 18.8 - - + -
298A ILE* 4.1 15.5 - - + +
299A LYS* 1.3 79.9 - - - +
301A THR* 1.3 74.9 + - - +
304A LYS* 4.3 15.3 - - + -
305A LEU* 4.5 4.9 - - + +
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Residues in contact with THR 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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273A LEU* 3.9 3.2 - - - +
277A GLN 3.7 9.6 - - - +
278A GLN* 3.9 21.3 - - + +
299A LYS* 5.8 2.7 - - + -
300A VAL* 1.3 83.7 - - - +
302A ARG* 1.3 64.7 + - - +
303A ALA* 3.5 9.9 + - - +
304A LYS* 3.0 30.8 + - - +
305A LEU 3.4 8.7 + - - -
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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