Contacts of the strand formed by residues 277 - 282 (chain B) in PDB entry 1NZL
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 THR 277 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268B LEU* 3.5 13.3 - - + +
273B ASN* 3.6 18.0 - - - +
274B PRO* 2.8 40.3 + - - +
275B ARG 3.8 0.2 + - - -
276B GLY* 1.3 77.5 - - - +
278B PHE* 1.3 63.2 + - - +
294B VAL* 3.4 0.5 - - - -
295B SER* 2.9 32.1 + - - -
348B THR* 3.8 0.2 + - - -
349B ASN* 3.0 27.0 + - - +
351B CYS* 3.5 24.5 - - - -
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Residues in contact with PHE 278 (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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254B TRP* 3.7 18.4 - + + -
268B LEU* 3.7 2.5 - - - -
276B GLY 3.6 9.4 - - - -
277B THR* 1.3 77.0 - - - +
279B LEU* 1.3 69.3 + - - +
280B VAL* 4.8 0.2 - - + -
292B LEU* 3.7 16.6 - - + -
293B SER 3.1 14.4 - - - +
294B VAL* 4.1 2.9 - - + -
333B VAL* 3.6 37.5 - - + -
337B SER* 4.8 2.5 - - - -
347B LEU* 3.7 37.2 - - + -
348B THR 4.6 0.7 - - - -
349B ASN* 2.8 33.9 + - - -
350B VAL* 3.8 21.2 - - + +
351B CYS* 2.9 27.1 + - - +
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Residues in contact with LEU 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B TRP 3.3 6.1 - - - -
256B PHE* 3.6 38.8 - - + -
259B ILE* 4.6 0.9 - - + -
264B SER* 4.0 13.7 - - - -
267B LEU* 4.4 6.5 - - + -
268B LEU* 4.0 15.9 - - + -
278B PHE* 1.3 82.3 - - - +
280B VAL* 1.3 66.9 + - - +
281B ARG* 3.8 33.4 - - + -
292B LEU* 3.6 4.5 - - - +
293B SER* 3.0 38.6 + - - +
351B CYS* 4.0 23.1 - - + -
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Residues in contact with VAL 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B TRP* 2.8 36.1 + - + -
255B TYR* 3.4 18.4 - - + -
256B PHE* 2.8 26.3 + - - +
278B PHE* 4.7 1.3 - - + -
279B LEU* 1.3 78.1 - - - +
281B ARG* 1.3 69.0 + - - +
290B TYR* 4.5 1.3 - - + -
291B CYS 3.2 10.8 - - - +
292B LEU* 3.9 15.0 - - + -
310B ILE* 4.1 17.0 - - + -
329B LEU* 4.3 16.4 - - + -
332B LEU* 5.6 0.7 - - + -
333B VAL* 3.9 15.7 - - + -
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Residues in contact with ARG 281 (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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255B TYR* 4.3 5.4 - - - -
257B GLY 3.2 15.5 - - - +
259B ILE* 3.5 35.1 + - + +
260B THR 4.2 0.2 - - - -
261B ARG* 3.8 19.6 - - - +
264B SER* 3.4 8.9 + - - -
279B LEU* 3.8 11.2 - - + -
280B VAL* 1.3 74.5 - - - +
282B GLU* 1.3 69.6 + - - +
284B GLU* 4.4 1.6 - - - +
290B TYR* 3.2 13.7 - - - +
291B CYS* 2.7 47.2 + - + +
293B SER* 3.0 13.3 + - - -
307B HIS* 3.0 31.7 + - - -
500C PTR 2.8 41.4 + - - -
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Residues in contact with GLU 282 (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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255B TYR* 3.5 20.8 + - - +
257B GLY* 2.8 17.4 + - - +
258B LYS* 3.0 50.1 + - + +
259B ILE 4.4 4.0 - - - +
281B ARG* 1.3 93.8 + - - +
283B SER* 1.3 66.6 + - - +
284B GLU* 3.7 1.4 + - - +
289B ALA 3.8 7.0 - - - +
290B TYR* 4.1 12.8 - - + -
291B CYS 4.6 0.4 - - - -
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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