Contacts of the strand formed by residues 368 - 377 (chain A) in PDB entry 1E8U
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 368 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319A GLY* 3.2 3.1 - - - -
320A LEU* 2.9 39.0 + - + +
327A ASP* 2.6 53.2 + - - +
330A GLN* 3.6 36.2 + - - +
331A GLU* 3.8 19.2 - - - +
332A GLY 4.5 3.2 - - - +
333A LYS 5.2 3.4 + - - -
356A LYS 5.6 1.6 + - - -
359A TYR* 3.1 28.7 - - + +
360A LYS* 3.3 39.1 - - + +
366A GLY 3.6 2.6 + - - -
367A LYS* 1.3 70.7 - - - +
369A ILE* 1.3 63.6 + - - +
370A GLN* 3.4 17.9 + - - +
393A ASN* 4.0 5.7 - - - +
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Residues in contact with ILE 369 (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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262A TYR* 3.4 38.1 - - + +
317A TYR* 4.7 6.7 - - + -
318A GLY 3.2 10.5 - - - +
359A TYR* 2.9 12.4 + - - +
361A PRO* 3.7 29.2 - - + -
364A PHE* 3.8 20.6 - - + -
367A LYS 3.6 11.4 - - - +
368A ARG* 1.3 74.2 - - - +
370A GLN* 1.3 59.9 + - - +
398A MET* 3.5 21.3 - - + +
399A GLY 2.9 42.1 + - - +
466A VAL* 5.3 0.4 - - + -
1570A SLB 6.3 1.6 - - - -
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Residues in contact with GLN 370 (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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295A TRP* 3.7 20.6 - - + -
317A TYR* 3.2 25.6 - - - +
318A GLY 2.8 13.2 + - - -
320A LEU* 3.7 20.8 - - + +
330A GLN* 3.2 28.8 + - - +
368A ARG* 3.4 7.9 + - - -
369A ILE* 1.3 71.6 - - - +
371A GLN* 1.3 83.6 + - - +
390A VAL* 3.6 14.2 - - + +
391A PRO 3.4 6.7 + - - -
393A ASN* 3.0 41.5 + - - -
396A THR* 4.3 1.6 + - - -
399A GLY* 3.5 6.3 - - - -
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Residues in contact with GLN 371 (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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315A SER* 4.1 9.4 - - - -
316A VAL 3.2 22.5 + - - +
370A GLN* 1.3 97.6 + - - +
372A ALA* 1.3 70.2 + - - +
373A ILE* 5.8 0.2 - - + -
390A VAL* 3.9 0.7 - - - +
391A PRO* 3.4 10.8 - - + +
396A THR* 4.2 28.7 - - + +
397A LEU 4.3 1.5 + - - +
399A GLY* 3.4 8.5 - - - +
400A ALA 3.1 34.6 + - - +
401A GLU 4.9 0.6 + - - -
402A GLY* 5.7 0.6 - - - -
413A LEU* 4.6 14.8 - - + +
415A GLN* 3.0 34.1 + - - +
438A LEU* 5.1 3.8 - - + -
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Residues in contact with ALA 372 (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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295A TRP* 3.7 25.4 - - + -
315A SER* 3.7 0.9 - - - -
316A VAL* 2.8 34.5 + - + +
371A GLN* 1.3 83.8 - - - +
373A ILE* 1.3 70.9 + - - +
388A LEU* 3.8 17.0 - - + -
389A THR 3.3 13.7 - - - +
390A VAL* 4.4 2.7 - - + -
391A PRO* 3.9 3.1 - - - -
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Residues in contact with ILE 373 (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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313A TRP* 4.0 29.4 - - + -
314A PHE 3.5 10.5 - - - +
315A SER* 4.9 0.7 - - - -
371A GLN* 5.6 1.3 - - + +
372A ALA* 1.3 80.8 - - - +
374A LEU* 1.3 64.1 + - - +
375A SER 4.2 0.2 + - - -
387A VAL 3.7 1.2 - - - +
388A LEU* 3.5 3.3 - - - -
389A THR* 2.6 49.5 + - - +
391A PRO* 4.5 8.3 - - + -
404A ILE* 4.5 18.4 - - + -
413A LEU* 5.0 4.0 - - + -
429A MET* 4.0 15.9 - - - -
436A ALA* 3.8 21.3 - - + -
438A LEU* 4.0 27.8 - - + -
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Residues in contact with LEU 374 (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 LEU* 4.0 23.6 - - + -
270A MET* 5.3 0.7 - - - -
286A LEU* 4.1 22.9 - - + -
291A LEU* 3.7 24.7 - - + -
292A PHE* 4.7 9.0 - - + -
312A VAL 3.7 1.0 - - - +
313A TRP* 3.5 0.9 - - - -
314A PHE* 2.8 43.4 + - + +
316A VAL* 4.1 8.5 - - + +
372A ALA 4.4 0.2 - - - -
373A ILE* 1.3 75.0 - - - +
375A SER* 1.3 61.2 + - - +
376A ILE* 4.1 15.7 - - + -
386A PRO* 4.2 2.7 - - + -
387A VAL 3.5 27.8 - - - +
388A LEU* 4.0 15.5 - - + +
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Residues in contact with SER 375 (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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311A ARG* 2.7 35.2 + - - -
312A VAL 3.1 5.6 - - - -
313A TRP* 3.4 37.0 - - - -
373A ILE 4.2 0.4 - - - -
374A LEU* 1.3 72.1 - - - +
376A ILE* 1.3 68.2 + - - +
387A VAL 2.9 29.7 + - - -
434A LYS 2.9 17.5 + - - -
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Residues in contact with ILE 376 (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 LEU* 4.5 7.6 - - + -
272A HIS* 3.7 45.3 - - + +
286A LEU* 4.6 7.4 - - + -
311A ARG* 2.9 8.9 - - - +
312A VAL* 2.7 49.7 + - + +
314A PHE* 4.8 5.4 - - + -
374A LEU* 4.1 25.4 - - + -
375A SER* 1.3 82.0 - - - +
377A LYS* 1.3 72.0 + - - +
383A GLY 3.9 3.6 - - - -
384A GLU 3.3 24.0 - - - +
385A ASP 4.4 0.4 - - - -
386A PRO* 4.5 7.2 - - + -
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Residues in contact with LYS 377 (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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272A HIS* 4.7 3.3 - - - -
309A ASP 4.6 2.8 + - - -
310A GLY* 3.3 32.9 + - - +
311A ARG* 3.9 26.9 - - + +
312A VAL* 5.4 0.2 - - - -
376A ILE* 1.3 81.1 - - - +
378A VAL* 1.3 71.6 + - - +
379A SER* 3.4 5.6 + - - -
381A SER 4.4 2.9 - - - +
384A GLU* 3.0 49.3 + - + +
385A ASP* 4.4 5.4 - - + +
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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