Contacts of the strand formed by residues 302 - 312 (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 GLY 302 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297B PHE* 3.4 28.7 - - - -
298B ASP 2.9 15.4 + - - -
299B ASN 4.3 3.3 - - - -
300B ALA 3.4 2.0 + - - -
301B LYS* 1.3 75.0 - - - +
303B LEU* 1.3 60.6 + - - -
304B ASN* 3.0 20.1 - - - +
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Residues in contact with LEU 303 (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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269B LEU* 3.5 40.6 - - + +
270B ASN 4.9 1.3 - - - +
271B PRO* 4.3 21.5 - - + +
273B ASN 5.0 10.5 - - - +
275B ARG* 6.3 3.6 - - - +
295B SER* 6.0 4.9 - - - -
296B ASP 3.5 11.4 - - - +
297B PHE* 3.7 17.4 - - + -
301B LYS 3.8 5.0 + - - +
302B GLY* 1.3 70.9 - - - -
304B ASN* 1.3 59.2 + - - +
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Residues in contact with ASN 304 (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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269B LEU* 3.8 6.7 - - - +
295B SER* 3.6 3.1 - - - -
296B ASP* 2.7 46.1 + - - +
297B PHE* 3.7 3.5 + - - -
298B ASP* 4.0 4.0 - - - +
301B LYS* 4.0 30.6 - - + +
302B GLY 3.0 14.8 - - - +
303B LEU* 1.3 74.6 - - - +
305B VAL* 1.3 64.8 + - - +
306B LYS* 2.7 37.4 + - - +
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Residues in contact with VAL 305 (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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265B GLU* 4.2 17.7 - - + +
268B LEU* 3.9 33.0 - - + -
269B LEU* 3.7 27.5 - - + +
294B VAL 3.4 11.0 - - - +
295B SER* 4.6 2.5 - - - -
304B ASN* 1.3 81.7 + - - +
306B LYS* 1.3 73.3 + - - +
307B HIS* 3.5 40.3 - - + +
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Residues in contact with LYS 306 (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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292B LEU 3.5 2.3 - - - +
293B SER* 3.4 3.6 - - - -
294B VAL* 2.9 33.0 + - - +
296B ASP* 3.1 26.3 + - + -
298B ASP* 5.0 3.8 + - - -
301B LYS* 4.5 15.0 - - - +
304B ASN* 2.7 30.9 + - - +
305B VAL* 1.3 76.1 - - - +
307B HIS* 1.3 61.6 + - - +
308B TYR* 3.8 22.2 - - + +
344B CYS* 3.5 27.4 - - + -
501C GLU* 3.4 36.1 - - + +
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Residues in contact with HIS 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B ARG* 3.5 33.4 - - + +
264B SER* 3.4 15.5 - - - -
265B GLU* 2.9 27.9 + - + +
281B ARG* 3.0 17.9 + - - -
291B CYS* 3.7 9.4 - - - -
292B LEU 3.7 2.7 - - - -
293B SER* 2.8 28.0 + - - -
305B VAL* 3.5 26.8 - - + +
306B LYS* 1.3 71.1 - - - +
308B TYR* 1.3 57.4 + - - +
499C GLN 4.6 2.6 + - - +
500C PTR 3.2 16.6 - - + -
501C GLU* 2.7 33.6 + - - +
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Residues in contact with TYR 308 (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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291B CYS* 3.2 3.2 - - - -
292B LEU* 2.8 47.9 + - + +
294B VAL* 4.5 7.4 - - + -
306B LYS* 3.8 18.6 - - + -
307B HIS* 1.3 72.8 - - - +
309B LYS* 1.3 62.8 + - - +
310B ILE* 3.5 1.7 + - - +
320B ILE* 3.8 33.9 - - + -
342B GLY 4.6 1.2 + - - -
343B LEU* 3.6 33.6 - - + -
344B CYS* 2.9 37.7 + - - +
500C PTR 4.1 1.6 - - - -
501C GLU* 3.1 48.8 - - + +
502C PTR 4.3 2.9 - - - -
503C ILE* 4.0 12.1 - - + -
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Residues in contact with LYS 309 (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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283B SER* 4.4 1.3 - - - +
285B THR* 4.7 1.0 + - - -
286B THR* 2.8 34.2 + - - +
289B ALA* 4.2 10.8 - - + -
290B TYR 3.6 10.3 - - - +
307B HIS 3.9 0.2 + - - -
308B TYR* 1.3 71.8 - - - +
310B ILE* 1.3 63.0 + - - +
311B ARG* 3.5 47.9 + - + +
319B TYR 3.7 0.5 - - - +
320B ILE* 3.6 23.8 - - - +
500C PTR 3.6 53.1 - - + +
501C GLU 4.6 2.4 + - - -
502C PTR 4.8 8.4 + - - +
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Residues in contact with ILE 310 (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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280B VAL* 4.1 9.4 - - + -
289B ALA* 3.5 5.0 - - - +
290B TYR* 2.7 45.2 + - + +
291B CYS 3.8 7.9 - - - +
292B LEU* 3.8 27.1 - - + +
308B TYR 3.9 8.3 - - - +
309B LYS* 1.3 72.8 - - - +
311B ARG* 1.3 63.3 + - - +
318B PHE* 4.0 15.7 - - + -
319B TYR 3.4 6.5 - - - +
320B ILE* 3.9 13.9 - - + -
329B LEU* 3.9 31.9 - - + -
332B LEU* 3.9 27.1 - - + -
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Residues in contact with ARG 311 (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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286B THR* 4.4 14.1 - - - +
289B ALA* 4.7 6.0 - - + +
309B LYS* 3.5 40.0 - - + +
310B ILE* 1.3 76.8 - - - +
312B LYS* 1.3 61.4 + - - +
313B LEU* 4.2 0.4 - - + -
318B PHE* 3.3 6.1 - - - +
319B TYR* 2.9 73.6 + - + +
320B ILE 6.1 0.2 - - - -
502C PTR 3.0 31.7 + - - -
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Residues in contact with LYS 312 (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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288B GLY 4.2 18.3 + - - +
290B TYR* 5.0 4.0 - - + -
310B ILE 4.1 0.4 + - - -
311B ARG* 1.3 77.4 - - - +
313B LEU* 1.3 81.0 + - - +
314B ASP* 3.9 6.6 + - - +
316B GLY 3.1 14.7 + - - -
317B GLY* 3.4 15.3 - - - +
318B PHE* 3.5 47.1 - - + -
327B SER 5.8 0.2 - - - -
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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