Contacts of the strand formed by residues 273 - 279 (chain A) in PDB entry 4NZP
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 LYS 273 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265A VAL* 4.1 21.5 - - + +
266A GLU 3.3 7.9 - - - +
267A ASN* 2.6 40.0 + - - +
268A ARG* 5.2 0.2 - - - -
272A MET* 1.3 101.7 - - + +
274A SER* 1.3 62.3 + - - +
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Residues in contact with SER 274 (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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192A GLU* 4.0 9.9 + - - -
265A VAL* 3.1 4.6 - - - -
266A GLU* 2.9 39.5 + - - +
268A ARG* 3.1 44.9 + - - -
273A LYS* 1.3 76.7 - - - +
275A ARG* 1.3 65.0 + - - +
276A GLY 3.9 1.4 + - - -
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Residues in contact with ARG 275 (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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191A TYR 4.4 0.3 - - - +
192A GLU* 3.9 17.2 - - - +
193A GLY 5.1 0.5 + - - -
196A LEU* 3.1 51.4 + - - +
197A GLU* 5.0 4.4 - - - +
198A ASP 2.7 29.3 + - - -
199A PRO* 3.5 21.6 + - + +
201A HIS 2.8 21.6 + - - -
202A ALA* 4.2 0.8 - - - +
203A PRO* 3.9 8.9 - - - +
263A ASP* 2.7 40.6 + - - +
264A ILE 3.5 10.3 - - - +
265A VAL* 3.9 18.8 - - + +
274A SER* 1.3 76.2 + - - +
276A GLY* 1.3 63.9 + - - +
277A CYS* 4.4 0.4 - - - -
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Residues in contact with GLY 276 (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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191A TYR 3.3 11.7 - - - -
192A GLU* 4.2 7.0 - - - -
196A LEU* 4.7 0.7 - - - -
263A ASP* 3.9 2.3 - - - +
264A ILE 2.9 32.4 + - - +
266A GLU* 5.0 2.2 + - - -
274A SER 3.9 1.8 + - - -
275A ARG* 1.3 77.0 - - - +
277A CYS* 1.3 65.4 + - - -
278A TYR* 3.9 18.6 - - - -
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Residues in contact with CYS 277 (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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190A SER* 3.6 0.5 + - - -
191A TYR* 2.8 35.5 + - + +
196A LEU* 3.8 29.8 - - + +
203A PRO* 4.2 3.4 - - - -
207A MET* 3.8 27.1 - - + -
208A TRP* 3.8 11.9 - - + -
262A LEU 3.2 9.4 - - - +
263A ASP* 3.8 29.4 - - - -
275A ARG* 4.4 0.2 - - - -
276A GLY* 1.3 73.0 - - - -
278A TYR* 1.3 67.8 + - - +
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Residues in contact with TYR 278 (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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91A TYR* 3.4 30.7 - + + -
95A THR* 4.8 1.8 - - - -
188A HIS* 3.3 25.1 - + + -
189A ILE 3.4 4.5 - - - +
190A SER* 3.4 23.6 + - - -
191A TYR* 4.8 0.4 - - - -
192A GLU* 4.5 8.5 + - - -
208A TRP* 3.8 2.4 - - - -
260A GLY 3.3 3.5 - - - +
261A ARG* 3.4 2.6 - - - -
262A LEU* 3.0 55.6 + - + -
264A ILE* 3.8 17.0 - - + -
266A GLU* 2.4 37.1 + - - -
276A GLY* 3.9 18.5 - - - -
277A CYS* 1.3 79.9 - - - +
279A GLU* 1.3 63.9 + - - +
280A THR* 4.0 11.9 - - - +
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Residues in contact with GLU 279 (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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188A HIS* 3.1 6.8 - - - -
189A ILE* 3.0 33.7 + - + +
191A TYR* 2.6 31.5 + - + -
208A TRP* 3.6 35.2 - - + +
209A ARG 4.2 0.9 - - - -
210A TRP* 3.1 33.2 + - + +
211A SER* 2.8 39.4 + - - +
259A ILE 6.0 0.2 - - - +
260A GLY 3.6 3.4 - - - -
261A ARG* 4.4 2.9 - - + -
278A TYR* 1.3 71.0 - - - +
280A THR* 1.3 60.7 + - - +
281A PRO* 3.3 9.6 - - + +
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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