Contacts of the strand formed by residues 284 - 298 (chain A) in PDB entry 4R2G
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 ILE 284 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A ILE* 4.0 20.0 - - + -
273A ARG 3.8 6.3 - - - +
274A SER* 4.2 11.0 - - - -
277A PHE* 4.0 25.8 - - + +
282A LYS 4.1 8.3 - - - +
283A THR* 1.3 71.0 - - - +
285A ILE* 1.3 73.7 + - - +
286A VAL* 3.9 7.7 + - + +
349A LEU* 4.6 5.6 - - + -
353A PHE* 4.6 1.6 - - + -
453A LEU* 3.8 1.4 - - - -
454A LEU* 2.9 43.7 + - + +
455A THR* 5.3 0.7 - - - -
456A ARG* 4.2 15.5 - - + +
468A PHE* 3.6 34.5 - - + -
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Residues in contact with ILE 285 (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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95A MET* 4.1 15.5 - - + -
96A TRP* 3.9 26.5 - - + -
260A LEU* 4.5 4.5 - - + -
272A ILE* 3.4 2.9 - - - -
273A ARG* 2.9 52.8 + - + +
283A THR* 3.5 3.6 + - + +
284A ILE* 1.3 74.0 - - - +
286A VAL* 1.3 69.7 + - - +
287A GLN* 5.7 0.7 - - + -
452A LEU 3.7 8.3 - - - +
453A LEU* 3.8 15.5 - - + -
477A ASP* 3.5 33.4 - - + +
480A ARG* 4.2 1.3 - - + -
481A SER* 4.1 22.4 - - - +
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Residues in contact with VAL 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A LEU* 4.6 1.2 - - - +
270A VAL* 4.4 2.7 - - + -
271A VAL 3.8 2.7 - - - +
272A ILE* 3.8 26.9 - - + -
284A ILE* 4.1 9.9 - - + +
285A ILE* 1.3 85.2 - - - +
287A GLN* 1.3 62.9 + - - +
288A LEU* 3.6 22.0 - - + -
345A ILE* 3.9 19.1 - - + -
349A LEU* 6.3 0.2 - - + -
451A GLY* 3.0 7.3 - - - -
452A LEU* 2.9 42.1 + - + +
454A LEU* 3.9 27.4 - - + -
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Residues in contact with GLN 287 (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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264A SER* 2.6 32.0 + - - +
265A LEU 3.5 3.0 + - - -
266A ALA* 3.4 29.3 - - + +
270A VAL* 3.2 7.3 - - - +
271A VAL* 2.9 45.9 + - + +
273A ARG* 2.8 33.3 + - - +
285A ILE* 5.7 1.6 - - + -
286A VAL* 1.3 75.3 - - - +
288A LEU* 1.3 64.3 + - - +
450A THR 4.0 7.2 - - - +
481A SER 4.7 12.2 + - - +
482A GLU* 4.9 0.2 + - - -
484A TYR* 3.7 21.6 + - - -
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Residues in contact with LEU 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A LEU* 2.7 29.2 - - + +
266A ALA* 3.3 12.6 + - - -
270A VAL* 4.1 8.3 - - + -
286A VAL* 3.6 28.7 - - + +
287A GLN* 1.3 77.2 - - - +
289A ASN* 1.3 56.9 + - - +
290A GLU 3.7 15.5 - - - +
292A VAL* 5.1 2.7 - - + +
341A THR* 3.9 22.4 - - + +
344A GLN* 5.7 0.7 - - - +
345A ILE* 4.0 12.8 - - + -
449A ILE* 3.5 28.9 - - + +
450A THR 3.7 11.9 + - - +
451A GLY 4.0 6.7 - - - +
452A LEU* 3.9 18.2 - - + -
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Residues in contact with ASN 289 (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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265A LEU* 3.6 9.9 - - - +
266A ALA* 3.7 15.9 - - - +
267A GLU 4.6 1.2 - - - -
268A GLU* 2.6 35.6 + - - +
269A LYS* 4.5 1.3 - - - -
270A VAL* 3.5 20.4 - - + +
288A LEU* 1.3 74.5 - - - +
290A GLU* 1.3 70.7 + - + +
344A GLN* 3.9 18.8 + - - +
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Residues in contact with GLU 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A LEU* 3.6 11.2 - - + -
288A LEU* 3.7 16.3 - - - +
289A ASN* 1.3 87.7 + - + +
291A SER* 1.3 67.3 + - - +
292A VAL* 4.0 4.5 + - + +
341A THR* 4.7 4.8 + - - +
344A GLN* 4.3 20.8 + - - +
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Residues in contact with SER 291 (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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265A LEU* 3.4 21.8 - - - +
290A GLU* 1.3 81.5 - - - +
292A VAL* 1.3 62.4 + - - +
293A LYS* 4.2 6.8 + - - -
337A GLN* 4.9 6.6 + - - +
448A ASN* 3.4 28.8 + - - +
449A ILE 3.5 11.7 - - - -
450A THR* 4.4 5.8 - - - -
520A NAG 3.8 16.2 + - - -
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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
----------------------------------------------------------
288A LEU* 5.2 1.3 - - + -
290A GLU* 4.7 3.4 - - + +
291A SER* 1.3 76.9 - - - +
293A LYS* 1.3 63.7 + - - +
333A ILE* 3.6 30.5 - - + -
334A SER 5.3 0.2 - - - +
337A GLN* 3.6 34.8 - - + +
338A TRP* 4.2 11.0 - - + +
341A THR* 3.1 32.1 - - + +
448A ASN* 3.9 0.9 - - - -
449A ILE* 2.4 52.7 + - + +
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Residues in contact with LYS 293 (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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291A SER* 4.2 6.0 + - - -
292A VAL* 1.3 85.8 - - - +
294A ILE* 1.3 60.8 + - - +
295A ASN* 4.8 1.5 + - - +
332A ASN 3.7 3.7 - - - +
333A ILE* 3.7 11.8 - - - +
334A SER 4.6 1.9 + - - -
337A GLN* 3.8 24.0 + - - +
446A SER* 5.3 4.5 - - - -
447A SER 4.7 1.1 - - - -
448A ASN* 3.8 24.6 - - + +
520A NAG 5.9 3.4 - - - -
1T NAG 4.0 54.5 + - - +
2T NAG 4.8 6.9 + - - -
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Residues in contact with ILE 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A LEU* 4.0 6.5 - - + -
261A LEU* 3.6 20.6 - - + -
293A LYS* 1.3 76.0 - - - +
295A ASN* 1.3 64.6 + - - +
296A CYS* 4.2 8.0 - - - -
331A CYS* 4.2 20.0 - - + -
332A ASN 3.2 9.6 - - - +
333A ILE* 3.9 21.8 - - + -
374A HIS* 3.6 32.1 - - + +
416A LEU* 4.6 1.1 - - + -
445A CYS 3.9 1.2 - - - +
446A SER* 3.2 2.9 - - - -
447A SER* 2.5 66.7 + - - +
449A ILE* 3.8 11.7 - - + -
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Residues in contact with ASN 295 (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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294A ILE* 1.3 76.9 - - - +
296A CYS* 1.3 63.1 + - - +
331A CYS* 3.2 3.3 - - - -
332A ASN* 2.8 35.9 + - + -
445A CYS 3.9 1.5 - - - -
446A SER* 2.3 35.3 - - - -
1S NAG 3.3 27.4 - - + +
1T NAG 1.5 59.3 + - - +
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Residues in contact with CYS 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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294A ILE* 4.2 12.8 - - - -
295A ASN* 1.3 75.8 - - - +
297A THR* 1.3 65.7 + - - +
330A HIS 3.3 2.7 - - - +
331A CYS* 2.2 50.0 - - - -
376A PHE* 3.3 27.6 - - + -
378A CYS* 5.4 0.2 - - - -
383A PHE* 4.2 7.2 - - + -
444A ARG* 3.4 2.6 - - - +
445A CYS* 2.9 44.2 + - - +
447A SER* 6.0 0.7 - - - -
1S NAG 5.3 0.4 - - - -
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Residues in contact with THR 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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296A CYS* 1.3 78.3 - - - +
298A ARG* 1.3 69.7 + - - +
299A PRO* 3.7 10.8 - - + +
327A ARG* 6.1 0.2 - - - +
329A ALA* 3.1 6.8 - - - +
330A HIS* 3.0 61.3 + - + +
383A PHE* 3.5 8.0 - - - -
442A GLN* 4.5 3.8 + - - +
443A ILE 3.4 13.1 + - - -
444A ARG* 3.9 20.0 + - - +
1S NAG 4.5 11.4 - - + +
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Residues in contact with ARG 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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297A THR* 1.3 75.7 + - - +
299A PRO* 1.3 67.9 + - + +
300A SER* 2.6 48.2 + - - +
301A ASN* 3.5 11.9 - - - +
302A ASN* 4.0 17.0 - - - +
327A ARG 5.7 0.4 - - - +
329A ALA* 3.8 10.5 - - + +
381A GLU* 2.4 30.6 + - - -
383A PHE* 3.6 5.0 - - + -
420A ILE* 3.5 28.0 - - + -
438A PRO* 4.8 5.1 - - - +
439A ILE 5.4 0.4 + - - -
440A LYS* 5.2 3.0 - - - +
441A GLY 3.2 28.5 + - - +
442A GLN* 4.2 1.0 - - - +
443A ILE* 3.4 36.0 + - + +
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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