Contacts of the strand formed by residues 270 - 282 (chain A) in PDB entry 4NTW
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 PHE 270 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266A VAL* 5.6 0.2 - - - +
267A ALA* 3.9 17.7 - - + +
268A PRO 3.3 16.2 - - - -
269A GLY* 1.3 86.6 - - - +
271A GLN* 1.3 60.5 + - - +
272A THR* 3.9 8.7 + - - +
377A MET* 3.2 41.7 - - + -
378A VAL 3.3 19.7 - - - +
379A LYS* 4.7 9.4 - - + -
380A ILE* 3.5 9.4 - - - +
405A LEU* 3.4 8.3 - - - +
406A VAL 3.1 21.7 + - - +
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Residues in contact with GLN 271 (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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220A GLU* 3.7 13.1 + - - -
270A PHE* 1.3 72.1 - - - +
272A THR* 1.3 62.5 + - - +
273A PHE* 3.5 29.4 + - + -
377A MET* 3.3 4.9 - - - -
378A VAL* 2.9 46.9 + - + +
379A LYS 5.5 0.2 - - - +
380A ILE* 4.0 9.3 - - + +
406A VAL* 3.2 24.8 - - + +
408A ASP* 2.9 29.3 + - - +
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Residues in contact with THR 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A GLY 5.6 0.7 - - - +
266A VAL* 3.9 21.6 - - + +
267A ALA 4.8 2.3 + - - -
270A PHE* 4.2 8.5 + - - +
271A GLN* 1.3 73.7 - - - +
273A PHE* 1.3 71.1 + - - +
274A VAL* 4.2 7.4 - - + -
375A LEU* 4.2 23.3 - - + -
376A SER 3.4 9.9 - - - +
377A MET* 3.7 18.7 - - + +
406A VAL 2.8 14.7 + - - -
407A LEU* 3.5 12.3 - - + +
408A ASP* 2.9 28.1 + - - +
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Residues in contact with PHE 273 (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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215A THR* 5.0 8.1 - - - -
271A GLN* 3.5 41.1 - - - -
272A THR* 1.3 73.2 - - - +
274A VAL* 1.3 60.1 + - - +
275A SER* 4.0 0.9 - - - -
374A GLU 3.4 1.7 - - - +
375A LEU* 3.1 8.1 - - - +
376A SER* 2.8 57.7 + - - +
377A MET 4.7 0.7 - - - -
378A VAL* 4.1 26.0 - - + -
408A ASP* 3.8 20.6 - - + -
410A PHE* 4.2 17.5 - + + -
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Residues in contact with VAL 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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250A ILE* 4.0 7.4 - - + -
264A PHE* 4.0 12.3 - - + -
272A THR* 4.2 2.7 - - + -
273A PHE* 1.3 77.0 - - - +
275A SER* 1.3 58.9 + - - +
276A CYS* 3.7 19.4 + - - -
373A LYS* 3.9 25.6 - - + -
374A GLU 3.6 2.2 - - - -
375A LEU* 3.9 21.8 - - + -
407A LEU* 3.8 28.0 - - + -
408A ASP 2.8 13.2 + - - +
409A ILE* 3.6 5.7 - - + -
410A PHE* 3.2 30.9 + - - +
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Residues in contact with SER 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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273A PHE* 4.0 1.0 - - - -
274A VAL* 1.3 71.5 - - - +
276A CYS* 1.3 61.0 + - - +
277A GLN* 5.7 0.2 - - - +
372A GLY 3.8 0.2 - - - +
373A LYS* 3.5 2.9 - - - -
374A GLU* 2.9 51.4 + - - +
410A PHE* 3.6 28.6 - - - -
412A GLU* 3.7 27.0 + - - +
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Residues in contact with CYS 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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89A PRO* 6.2 0.7 - - - -
250A ILE* 4.0 23.8 - - - -
274A VAL* 3.8 23.3 - - - -
275A SER* 1.3 77.4 + - - +
277A GLN* 1.3 66.8 + - - +
371A TYR* 4.8 6.1 - - + -
372A GLY 3.2 5.8 - - - +
373A LYS* 4.1 7.6 - - - -
409A ILE* 4.1 7.9 - - - -
410A PHE 2.8 21.3 + - - +
411A PHE* 3.5 27.8 - - + -
412A GLU* 3.0 22.4 + - - +
413A ALA 4.7 0.7 + - - +
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Residues in contact with GLN 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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276A CYS* 1.3 77.2 - - - +
278A GLU* 1.3 64.7 + - - +
279A GLN* 3.7 1.8 + - + +
370A ARG 3.6 0.2 - - - +
371A TYR* 3.3 5.3 - - - -
372A GLY* 2.9 40.8 + - - +
411A PHE* 4.5 3.1 - - - -
412A GLU* 3.4 39.4 + - + +
413A ALA* 5.7 4.4 - - - +
415A ASN 5.5 7.4 + - - +
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Residues in contact with GLU 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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86A LEU* 3.8 21.5 - - + +
87A THR 4.3 12.0 + - - +
277A GLN* 1.3 76.4 - - - +
279A GLN* 1.3 65.6 + - - +
280A ARG* 2.6 41.5 + - - +
369A THR* 3.7 24.5 - - + +
370A ARG 3.6 3.6 - - - -
371A TYR* 4.0 15.1 + - + -
411A PHE* 4.1 17.8 - - + -
415A ASN 4.5 5.1 + - - +
416A TYR* 3.5 15.9 - - + -
417A GLU* 3.3 21.0 + - - +
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Residues in contact with GLN 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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277A GLN* 4.8 2.0 - - + +
278A GLU* 1.3 76.6 - - - +
280A ARG* 1.3 65.1 + - - +
281A LEU* 3.6 27.0 - - + +
368A VAL 3.7 0.7 - - - +
369A THR* 3.4 3.3 - - - +
370A ARG* 2.8 74.3 + - + +
417A GLU* 3.3 36.2 + - + +
419A ILE* 3.7 18.1 - - + +
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Residues in contact with ARG 280 (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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85A ARG 5.5 0.4 + - - -
86A LEU* 4.2 9.7 - - - +
87A THR 5.9 1.0 - - - +
278A GLU* 2.6 31.0 + - - +
279A GLN* 1.3 73.2 - - - +
281A LEU* 1.3 63.8 + - - +
282A ILE* 4.1 8.4 + - + +
368A VAL 3.4 4.5 - - - +
369A THR* 4.4 12.3 - - - +
416A TYR* 3.1 57.3 + - + -
417A GLU 2.8 13.0 + - - +
418A THR* 3.2 11.6 - - + -
419A ILE* 2.9 26.3 + - - +
501A NAG 6.3 1.4 - - - -
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Residues in contact with LEU 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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279A GLN* 3.6 37.7 - - + +
280A ARG* 1.3 78.1 - - - +
282A ILE* 1.3 61.3 + - - +
283A TYR* 3.5 34.5 - - + +
366A CYS 3.7 3.3 - - - +
367A ASN* 3.7 1.6 - - - -
368A VAL* 2.7 49.7 + - + +
370A ARG* 4.4 13.9 - - + -
419A ILE* 3.3 27.6 - - + +
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Residues in contact with ILE 282 (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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280A ARG* 4.8 10.3 - - + +
281A LEU* 1.3 80.3 - - - +
283A TYR* 1.3 74.6 + - - +
284A LEU* 6.2 1.3 - - + -
366A CYS 3.4 7.4 - - - +
367A ASN* 4.3 10.3 - - - +
418A THR* 5.5 8.7 - - + -
419A ILE 2.8 11.9 + - - +
420A GLU* 3.5 39.5 - - + +
421A GLN* 2.9 31.1 + - - +
501A NAG 3.2 35.7 - - - +
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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