Contacts of the strand formed by residues 267 - 283 (chain A) in PDB entry 1IVV
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 ARG 267 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A ARG* 3.1 5.2 - - - +
264A ASP* 2.8 40.1 + - - +
266A ASP* 1.3 109.7 + - - +
268A LEU* 1.3 64.6 + - - +
269A ARG* 3.6 35.0 + - + +
444A ASP* 4.7 8.5 + - - -
502A SER* 5.8 0.2 + - - -
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Residues in contact with LEU 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A LYS 4.7 0.4 - - - +
244A SER* 3.9 21.5 - - - +
261A ALA* 3.2 34.5 - - + -
262A PHE 3.9 0.9 - - - -
263A ARG* 3.9 31.9 - - + +
266A ASP 3.9 1.6 + - - +
267A ARG* 1.3 73.2 - - - +
269A ARG* 1.3 60.2 + - - +
270A PRO* 3.6 8.3 - - + +
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Residues in contact with ARG 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A ALA* 3.2 3.6 - - - +
262A PHE* 2.8 49.1 + - + +
264A ASP* 2.8 50.6 + - + -
267A ARG* 3.8 24.6 - - + +
268A LEU* 1.3 73.0 - - - +
270A PRO* 1.3 64.4 - - - +
271A ILE* 4.0 2.5 - - - +
444A ASP* 2.9 43.0 + - - +
510A VAL* 3.6 11.1 - - - +
616A PHE* 2.9 63.1 + - + -
617A PHE* 4.1 3.2 - - - +
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Residues in contact with PRO 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ASN* 6.4 0.9 - - - -
260A ILE 3.8 6.7 - - - +
261A ALA* 3.9 5.4 - - + -
268A LEU* 3.6 11.2 - - + +
269A ARG* 1.3 88.2 - - + +
271A ILE* 1.3 59.4 + - - +
272A ILE 6.0 0.2 - - - +
442A ALA* 2.7 17.1 - - + +
443A ILE* 3.7 0.2 - - - -
444A ASP* 2.7 34.8 + - - +
445A GLY* 3.3 26.7 - - - +
616A PHE* 4.0 2.4 - - - -
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Residues in contact with ILE 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A TRP* 3.6 28.5 - - + -
260A ILE 2.9 10.3 + - - +
261A ALA 4.5 0.4 - - - -
262A PHE* 3.7 23.6 - - + +
269A ARG 4.0 3.6 - - - +
270A PRO* 1.3 80.1 - - - +
272A ILE* 1.3 68.5 + - + +
396A ILE* 3.7 24.2 - - + -
441A MET* 3.6 0.7 - - + +
442A ALA 2.9 24.0 + - - -
443A ILE* 3.2 19.9 + - + +
512A TYR* 3.6 38.8 - - + +
616A PHE* 3.9 16.2 - - + -
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Residues in contact with ILE 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ASN 3.7 0.5 - - - -
260A ILE* 2.8 48.1 + - + +
270A PRO* 6.0 0.2 - - - -
271A ILE* 1.3 90.0 - - + +
273A ASN* 1.3 63.1 + - - +
274A ARG 3.5 24.7 - - - +
275A ALA* 4.2 7.9 - - + -
388A TRP* 6.3 0.2 - - + -
396A ILE* 3.7 26.0 - - + -
439A LEU* 4.4 19.5 - - + -
440A ASP 3.4 16.4 - - - +
441A MET* 3.5 20.0 - - + -
442A ALA* 4.0 2.2 - - - +
611A LEU* 4.6 15.7 - - + -
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Residues in contact with ASN 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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12A PHE* 5.7 3.7 - - - -
49A ARG* 3.1 15.6 + - - +
257A LEU 4.7 0.2 - - - -
258A HIS* 3.5 4.9 + - - +
259A ASN* 2.8 44.5 + - - +
272A ILE* 1.3 72.6 - - - +
274A ARG* 1.3 59.1 + - - +
440A ASP* 2.6 40.1 + - - +
442A ALA* 3.6 10.0 - - + +
446A PHE* 3.8 30.2 - - + -
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Residues in contact with ARG 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ASP* 6.3 0.2 - - - +
250A ASP* 5.2 3.8 - - - +
253A GLU* 2.9 26.5 + - - -
256A VAL* 3.5 30.3 - - + +
257A LEU 3.4 6.1 - - - +
258A HIS* 3.7 18.9 - - - +
260A ILE* 5.9 0.2 - - - -
272A ILE* 3.4 6.1 - - - +
273A ASN* 1.3 84.0 - - - +
275A ALA* 1.3 63.0 + - - +
276A SER* 3.1 26.7 + - - -
438A ARG* 3.4 28.4 + - - +
440A ASP* 2.8 45.2 + - + +
551A ARG* 5.7 0.8 + - - +
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Residues in contact with ALA 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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256A VAL* 3.6 2.3 - - - +
257A LEU* 2.9 33.5 + - + +
260A ILE* 3.9 24.9 - - + +
272A ILE* 4.2 3.1 - - + -
274A ARG* 1.3 74.9 - - - +
276A SER* 1.3 64.6 + - - +
388A TRP* 3.8 28.5 - - + -
438A ARG 3.6 3.6 - - - -
439A LEU* 3.9 11.2 - - + -
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Residues in contact with SER 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A GLU* 2.9 25.7 + - - -
255A VAL 4.6 3.8 - - - -
256A VAL* 3.9 17.0 - - - -
274A ARG* 3.1 20.1 + - - -
275A ALA* 1.3 75.9 - - - +
277A ILE* 1.3 62.9 + - - +
278A ALA 3.4 0.3 + - - -
388A TRP* 3.9 8.9 - - - -
437A ALA* 3.2 4.3 - - - +
438A ARG* 2.6 47.4 + - - +
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Residues in contact with ILE 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A GLU* 3.5 26.3 + - - +
255A VAL 5.1 3.6 + - - -
276A SER* 1.3 75.4 - - - +
278A ALA* 1.3 60.3 + - - +
279A GLU 3.3 24.4 + - - +
280A MET* 4.6 1.8 - - + -
299A THR* 4.1 5.8 + - - +
386A PHE* 3.7 30.3 - - + -
388A TRP* 4.2 6.5 - - + +
398A PHE* 3.6 50.7 - - + -
435A PHE* 4.3 12.1 - - + -
436A SER 3.2 5.4 - - - +
437A ALA* 4.0 17.9 - - + -
588A PHE* 4.2 4.9 - - + -
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Residues in contact with ALA 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ARG* 5.1 0.5 + - - -
253A GLU* 3.5 18.6 - - - +
276A SER 3.4 2.6 + - - -
277A ILE* 1.3 73.4 - - - +
279A GLU* 1.3 65.2 + - - +
299A THR* 3.7 11.8 - - - +
436A SER* 2.9 8.1 + - - +
438A ARG* 3.7 26.0 - - + +
551A ARG 4.0 8.1 - - - +
552A TYR* 3.8 11.8 - - + +
553A PRO* 3.4 26.9 - - + +
585A TRP* 4.4 1.1 - - + -
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Residues in contact with GLU 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ARG* 4.7 1.2 + - - -
277A ILE* 3.2 9.9 - - - +
278A ALA* 1.3 81.5 - - - +
280A MET* 1.3 90.1 + - - +
281A VAL* 4.2 3.4 - - + -
297A PHE* 3.8 12.9 - - - +
299A THR* 3.3 11.7 + - - -
300A GLY* 2.9 39.6 + - - -
434A ILE 4.6 0.2 - - - -
436A SER* 3.0 25.8 + - - -
536A PHE* 3.7 25.1 - - + -
553A PRO* 3.4 19.5 - - + -
554A THR* 2.5 28.6 + - + +
558A VAL* 3.8 1.9 - - - +
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Residues in contact with MET 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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277A ILE* 4.6 2.2 - - + -
279A GLU* 1.3 89.1 + - - +
281A VAL* 1.3 63.6 + - - +
282A VAL* 4.4 4.5 - - + -
297A PHE* 3.5 0.7 - - - -
298A ASP* 3.1 46.4 + - + +
299A THR* 3.7 9.6 + - - +
304A VAL* 4.8 2.9 - - - -
384A TYR* 3.3 54.5 - - + +
386A PHE* 4.1 15.7 - - - -
433A HIS* 4.9 1.6 - - + +
434A ILE 3.2 11.2 - - - +
435A PHE* 3.6 37.5 - - + -
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Residues in contact with VAL 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A GLU* 4.2 0.7 - - + -
280A MET* 1.3 73.2 - - - +
282A VAL* 1.3 62.8 + - - +
283A PRO* 3.4 14.5 - - + +
295A ASN* 6.2 0.4 - - + -
296A TYR 3.2 4.9 - - - +
297A PHE* 3.4 42.8 - - + -
433A HIS* 3.5 1.6 - - - -
434A ILE* 2.8 59.3 + - + +
522A LEU* 4.9 1.6 - - + -
530A ILE* 5.3 3.4 - - + -
534A ALA* 3.9 7.6 - - + -
536A PHE* 3.5 24.2 - - + -
537A ALA* 4.3 9.6 - - + -
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Residues in contact with VAL 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 MET* 4.4 5.4 - - + -
281A VAL* 1.3 78.2 - - - +
283A PRO* 1.3 60.3 - - - +
284A TYR* 3.5 28.7 - - + +
295A ASN* 3.5 2.6 - - - -
296A TYR* 2.8 40.5 + - + -
298A ASP* 3.1 23.6 - - - +
382A DAH 4.8 2.0 - - + -
384A TYR* 3.5 19.3 - - - +
431A HIS* 4.1 4.3 - - + -
432A GLN 3.1 13.2 - - - +
433A HIS* 3.8 24.2 - - + +
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Residues in contact with PRO 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A VAL* 3.4 16.4 - - + +
282A VAL* 1.3 88.3 - - - +
284A TYR* 1.3 63.7 + - - +
295A ASN* 3.2 21.8 - - + +
431A HIS* 3.1 4.7 - - - +
432A GLN* 3.0 52.0 + - + +
434A ILE* 4.9 0.2 - - + -
522A LEU* 3.7 24.5 - - + -
530A ILE* 4.2 15.3 - - + -
470B PHE* 4.5 2.9 - - + -
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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
------------------------------------------------------------
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