Contacts of the strand formed by residues 279 - 283 (chain A) in PDB entry 1NNC
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 SER 279 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A SER* 3.6 6.1 - - - -
278A CYS* 1.3 71.1 - - - +
280A CYS* 1.3 59.9 + - - +
281A TYR* 5.1 1.9 - - - -
288A THR 3.8 1.0 - - - +
289A CYS* 3.2 0.7 - - - -
290A THR* 2.9 31.9 + - - -
350A LYS* 2.8 25.3 + - - +
351A GLY 2.8 26.3 + - - -
352A PHE* 3.6 17.8 - - - +
353A SER 5.6 0.7 - - - +
408A GLY* 3.4 7.2 - - - -
409A SER* 3.6 13.7 + - - -
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Residues in contact with CYS 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TYR* 4.8 0.2 + - - -
226A GLN* 3.9 28.0 - - - -
228A SER* 4.5 0.8 + - - -
229A GLU* 4.4 14.7 + - - +
230A CYS* 5.4 1.3 - - - -
231A VAL* 4.0 20.5 - - + +
238A PRO 6.0 0.7 - - - -
278A CYS* 4.0 3.5 + - - -
279A SER* 1.3 74.6 - - - +
281A TYR* 1.3 62.5 + - - +
287A ILE* 4.1 4.9 - - + -
288A THR 3.2 4.0 - - - +
289A CYS* 2.0 47.8 - - - -
409A SER* 3.1 24.5 + - - +
410A PHE* 4.6 0.7 + - - -
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Residues in contact with TYR 281 (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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12A TYR* 3.4 13.7 - - - +
91A LEU* 4.2 6.5 - - + -
231A VAL* 3.9 7.2 - - - -
279A SER 5.1 1.3 - - - -
280A CYS* 1.3 77.5 - - - +
282A GLY* 1.3 65.3 + - - +
283A GLU* 3.9 22.8 + - + -
287A ILE* 3.4 3.8 - - - +
288A THR* 2.9 65.3 + - + +
290A THR* 5.4 1.3 - - - -
353A SER 3.4 22.9 - - - -
354A TYR* 3.5 41.3 - + + +
355A LEU* 3.0 33.7 + - - -
409A SER* 4.3 5.8 - - - +
410A PHE 5.5 1.3 - - - +
411A MET* 4.1 12.3 - - + -
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Residues in contact with GLY 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TYR* 3.0 13.8 + - - -
87A LEU* 3.9 21.3 - - - -
231A VAL* 4.1 3.0 - - - +
281A TYR* 1.3 76.4 - - - +
283A GLU* 1.3 67.5 - - - +
286A GLU 3.2 10.8 - - - -
287A ILE* 4.2 1.6 - - - -
411A MET* 3.2 19.5 - - - +
418A TYR* 3.5 6.8 - - - -
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Residues in contact with GLU 283 (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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87A LEU* 4.2 2.5 - - - +
89A LYS 3.4 13.0 - - - +
90A GLY* 4.2 11.8 - - - -
91A LEU* 4.1 17.7 + - + +
281A TYR* 3.9 23.5 + - + -
282A GLY* 1.3 75.9 - - - +
284A ARG* 1.3 86.9 + - - +
285A ALA 3.3 2.2 - - - -
286A GLU* 3.0 32.3 + - - +
288A THR* 4.8 5.0 + - - -
355A LEU 5.5 3.2 - - - +
356A ASP* 4.7 10.9 - - - +
418A TYR* 4.2 8.5 - - + -
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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