Contacts of the strand formed by residues 291 - 303 (chain A) in PDB entry 3NZI
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 291 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282A ILE* 3.2 4.1 - - - +
283A GLY 3.0 36.0 + - - -
285A PRO* 3.7 18.6 - - + +
288A LEU* 2.8 31.3 + - + +
289A GLN 4.5 0.3 + - - -
290A ASN* 1.3 76.2 - - - +
292A VAL* 1.3 71.4 + - - +
293A THR* 4.1 14.8 + - + -
327A ASN* 5.0 1.2 + - - +
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Residues in contact with VAL 292 (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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172A ILE* 5.0 11.9 - - + -
176A VAL* 4.3 24.7 - - + -
280A VAL* 3.8 16.6 - - + -
281A ALA 3.4 12.8 - - - +
282A ILE* 4.0 12.8 - - + -
290A ASN* 3.8 7.1 + - - +
291A THR* 1.3 76.9 - - - +
293A THR* 1.3 76.3 + - - +
294A THR* 5.4 1.3 - - + -
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Residues in contact with THR 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A VAL 3.7 0.7 - - - -
281A ALA* 2.8 43.6 + - - +
285A PRO* 6.0 2.5 - - + -
291A THR* 4.1 16.3 + - + -
292A VAL* 1.3 83.7 - - - +
294A THR* 1.3 65.1 + - - +
321A ALA* 4.4 0.2 - - - +
322A ILE* 2.8 44.0 + - + +
323A ILE* 4.2 0.7 - - - +
327A ASN* 5.6 2.6 + - - +
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Residues in contact with THR 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ILE* 4.1 29.0 - - + +
278A PHE* 5.3 3.3 - - - -
279A VAL 2.9 17.2 + - - -
280A VAL* 4.4 9.6 - - - -
292A VAL* 5.4 2.2 - - + -
293A THR* 1.3 81.6 - - - +
295A GLY* 1.3 64.8 + - - +
320A ASP 4.8 1.2 - - - +
321A ALA* 3.8 13.2 - - - +
322A ILE 5.0 0.9 + - - -
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Residues in contact with GLY 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A PHE* 3.4 7.6 - - - -
279A VAL* 3.0 26.2 + - - +
294A THR* 1.3 81.0 + - - +
296A ILE* 1.3 71.8 + - - +
320A ASP* 3.2 13.9 - - - -
321A ALA* 3.8 10.5 - - - +
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Residues in contact with ILE 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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276A GLY* 3.8 21.1 - - - +
277A GLU 3.0 9.0 - - - +
278A PHE* 3.7 25.8 - - + -
279A VAL* 3.7 8.8 - - - +
295A GLY* 1.3 81.5 - - - +
297A VAL* 1.3 67.6 + - - +
298A SER* 2.9 16.3 + - - +
319A THR* 3.3 12.7 + - - -
320A ASP* 2.7 33.4 + - - +
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Residues in contact with VAL 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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273A LEU* 3.5 31.2 - - + -
274A ARG 3.7 11.7 - - - +
275A PRO* 3.9 3.5 - - + +
276A GLY* 3.0 20.5 + - - +
277A GLU* 2.9 18.7 + - + +
279A VAL* 3.9 21.0 - - + +
296A ILE* 1.3 70.2 - - - +
298A SER* 1.3 61.5 + - - +
299A THR 3.6 27.6 - - - +
300A THR* 3.8 20.2 - - + +
317A ILE* 4.3 6.3 - - + -
318A GLN 3.5 5.8 - - - +
319A THR* 4.7 1.1 - - - +
332A LEU* 6.0 0.4 - - + -
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Residues in contact with SER 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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275A PRO* 5.6 3.0 - - - +
296A ILE* 2.9 11.0 + - - +
297A VAL* 1.3 71.7 - - - +
299A THR* 1.3 67.0 + - - -
318A GLN* 2.6 40.1 + - - -
319A THR* 3.6 0.8 - - - -
320A ASP* 3.2 32.6 + - - +
350A GLY 4.7 1.5 + - - -
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Residues in contact with THR 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A PRO* 5.4 4.3 - - - -
297A VAL* 3.3 7.4 - - - +
298A SER* 1.3 84.3 + - - +
300A THR* 1.3 65.9 + - - +
301A GLN 3.5 27.6 - - - +
302A ARG* 3.1 37.1 + - + +
316A TYR 4.3 0.3 - - - +
317A ILE* 3.7 1.0 - - - -
318A GLN* 2.9 38.7 + - - +
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Residues in contact with THR 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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270A SER 5.8 0.9 - - - -
273A LEU* 3.6 34.3 - - + +
274A ARG 3.8 3.1 - - - -
275A PRO* 3.7 30.1 - - + +
297A VAL* 3.8 11.2 - - + -
299A THR* 1.3 78.2 - - - +
301A GLN* 1.3 74.1 + - - +
315A ASP 5.1 0.7 - - - +
316A TYR 3.8 1.3 - - - +
317A ILE* 3.7 25.0 + - - +
356A PRO* 5.9 0.3 - - - +
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Residues in contact with GLN 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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270A SER 5.7 1.6 + - - -
271A SER* 5.7 9.1 + - - +
299A THR* 3.5 9.7 - - - +
300A THR* 1.3 94.4 + - - +
302A ARG* 1.3 60.2 + - - +
303A GLY 4.1 1.2 + - - -
306A GLU* 4.5 3.8 - - - +
315A ASP* 3.8 30.1 - - + +
316A TYR 3.9 1.6 - - - -
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Residues in contact with ARG 302 (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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299A THR* 3.1 33.7 + - + +
301A GLN* 1.3 73.2 - - - +
303A GLY* 1.3 61.8 + - - +
304A GLY 3.8 0.3 + - - -
306A GLU* 3.0 48.9 + - + +
307A LEU* 4.7 9.0 - - + +
315A ASP* 4.1 1.8 - - - -
316A TYR* 2.8 44.7 + - - +
318A GLN* 2.7 30.8 + - + +
353A PHE* 4.2 17.3 - - + -
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Residues in contact with GLY 303 (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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301A GLN 4.1 0.8 + - - -
302A ARG* 1.3 72.7 - - - +
304A GLY* 1.3 54.8 + - - -
305A LYS* 3.0 8.7 - - - -
306A GLU* 2.7 44.4 + - - +
307A LEU* 3.8 4.1 + - - +
314A MET 3.4 1.3 - - - -
315A ASP* 3.2 23.3 + - - -
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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