Contacts of the strand formed by residues 370 - 380 (chain A) in PDB entry 1EX0
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 TRP 370 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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279A PHE* 4.0 16.2 - + - -
314A CYS* 3.9 1.1 - - - -
339A PHE* 3.2 5.7 - - - -
340A SER* 2.8 47.0 + - - +
342A HIS* 3.6 29.7 - + + +
343A ASP* 4.5 3.0 + - - -
368A SER 4.5 6.1 - - - -
369A VAL* 1.3 73.7 - - - +
371A ASN* 1.3 63.3 + - - +
372A TYR 3.5 25.8 - - - +
373A HIS* 3.5 29.2 - - + -
398A THR* 4.3 7.0 - - + -
560A TYR* 3.4 30.7 - + - -
561A THR* 3.3 41.0 + - + -
11B ARG* 3.6 34.1 + - - +
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Residues in contact with ASN 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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215A GLY 3.7 17.9 - - - +
216A GLU* 4.7 4.8 - - + -
217A VAL 5.1 0.2 + - - -
338A TYR* 3.6 10.9 - - - +
339A PHE* 3.1 30.1 + - - -
369A VAL 3.4 5.5 + - - -
370A TRP* 1.3 71.0 - - - +
372A TYR* 1.3 64.7 + - + +
558A THR* 4.4 4.3 + - - -
559A PHE 5.2 0.4 - - - -
560A TYR* 3.0 19.2 + - - +
562A GLY* 5.2 3.9 - - - -
603A SER* 3.6 28.4 + - - -
604A LEU 5.0 0.5 - - - +
605A HIS* 5.3 2.8 - - - +
624A SER* 2.6 39.4 + - - -
626A VAL* 4.8 3.3 - - - +
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Residues in contact with TYR 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A PHE 4.0 10.3 - - - -
214A TYR* 3.4 22.4 - - + -
215A GLY* 3.3 25.1 - - - -
223A ARG* 3.6 14.9 + - - -
314A CYS* 4.7 0.2 - - - -
315A TRP* 3.9 8.3 - + - -
336A THR* 3.7 19.1 - - + -
337A ASN 3.2 8.5 - - - +
338A TYR* 3.9 9.9 - - + -
340A SER* 4.6 0.2 - - - -
370A TRP* 3.5 20.4 - - - +
371A ASN* 1.3 82.2 - - + +
373A HIS* 1.3 69.0 + - - +
374A CYS* 4.1 15.5 - - - -
560A TYR* 3.3 35.5 + + + -
601A GLN* 2.6 39.7 + - - -
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Residues in contact with HIS 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A CYS* 3.3 25.8 - - + +
336A THR* 3.7 0.6 - - - -
337A ASN* 2.9 33.9 + - - +
340A SER* 3.6 17.0 - - - +
342A HIS* 3.4 9.3 - + - -
370A TRP* 3.5 16.6 - + + -
372A TYR* 1.3 78.8 - - - +
374A CYS* 1.3 84.6 + - - +
375A TRP* 3.5 19.4 - + - -
396A ASP* 2.6 36.0 + - - -
398A THR* 3.6 13.0 - - + -
434A GLU* 3.4 21.1 - - - -
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Residues in contact with CYS 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A ILE* 4.3 7.0 - - - -
213A PHE 4.2 3.8 - - - -
314A CYS* 3.3 18.7 - - - +
315A TRP* 3.9 31.9 - - - -
318A ALA* 4.3 2.1 - - + +
334A ILE* 4.3 10.5 - - + -
335A VAL 3.2 7.9 - - - +
336A THR* 3.5 22.4 - - - -
372A TYR* 4.1 17.0 - - - -
373A HIS* 1.3 99.2 + - - +
375A TRP* 1.3 61.2 + - - +
396A ASP* 4.1 1.9 - - - +
398A THR* 4.5 0.7 + - - -
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Residues in contact with TRP 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ALA* 4.3 3.1 - - - -
334A ILE* 3.6 7.4 - - - +
335A VAL* 3.0 47.3 + - + +
337A ASN* 3.5 31.4 - - + -
340A SER* 3.8 4.9 - - - -
373A HIS* 3.5 23.8 - + - -
374A CYS* 1.3 75.2 - - - +
376A ASN* 1.3 87.7 + - - +
394A ALA* 4.0 11.1 - - + +
395A VAL 3.6 10.3 - - - +
396A ASP* 3.7 23.3 - - + +
397A SER 5.8 0.2 - - - +
431A VAL* 4.5 9.2 - - + -
434A GLU* 3.6 21.3 - - + -
435A VAL* 3.7 21.8 - - + -
464A ILE* 5.2 1.8 - - + -
481A TYR* 3.0 40.7 + + - -
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Residues in contact with ASN 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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318A ALA* 2.9 45.3 + - - +
321A PHE* 3.6 29.3 - - + +
322A ASN* 3.5 28.7 + - - +
325A LEU* 4.9 2.9 - - + +
333A ARG 3.5 4.3 - - - +
334A ILE* 3.8 4.0 - - - +
335A VAL* 5.3 0.2 - - - -
375A TRP* 1.3 88.7 - - - +
377A GLU* 1.3 66.3 + - - +
394A ALA* 3.5 1.6 - - - -
395A VAL* 3.0 36.3 + - + +
397A SER* 4.7 5.2 + - - -
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Residues in contact with GLU 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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332A ALA* 3.2 7.3 - - - +
333A ARG* 2.7 79.7 + - + +
335A VAL* 3.6 18.6 - - + +
376A ASN* 1.3 81.1 - - - +
378A ALA* 1.3 62.9 + - - +
392A TRP* 3.6 24.0 - - + +
393A GLN 3.3 9.0 - - - +
394A ALA* 4.4 2.0 - - - -
395A VAL* 5.6 0.2 - - - -
414A VAL* 3.5 7.7 - - + +
477A ILE* 4.3 0.3 - - - +
480A THR* 4.8 0.7 + - - -
481A TYR* 2.7 41.1 + - - +
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Residues in contact with ALA 378 (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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259A SER* 4.2 5.6 - - - +
325A LEU* 3.7 25.6 - - + -
330A ILE* 3.9 8.1 - - + -
331A PRO 3.4 4.7 - - - -
377A GLU* 1.3 76.8 - - - +
379A TRP* 1.3 61.0 + - - +
380A MET* 3.8 18.4 - - + -
392A TRP* 3.7 2.7 - - - -
393A GLN* 2.9 40.7 + - - +
395A VAL* 4.8 7.0 - - + -
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Residues in contact with TRP 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ALA 5.2 0.2 - - - -
193A VAL* 3.5 40.7 - - - +
194A TYR 2.8 20.9 + - - -
195A LEU* 3.6 32.2 - - + +
196A ASP* 5.3 6.1 - - - -
200A GLU* 5.8 1.1 - - - -
330A ILE* 4.1 0.5 - - - +
331A PRO* 2.9 31.9 + - + +
378A ALA* 1.3 70.5 - - - +
380A MET* 1.3 69.3 + - - +
391A GLY* 3.4 39.7 - - - -
392A TRP* 3.5 43.4 - + + -
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Residues in contact with MET 380 (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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192A ALA 3.4 12.3 - - - +
193A VAL* 4.4 1.3 - - + +
255A PRO* 3.7 18.2 - - + +
256A ILE* 3.5 39.9 - - + -
259A SER* 3.6 21.8 - - - +
330A ILE* 4.2 7.0 - - + -
378A ALA* 3.8 31.6 - - + +
379A TRP* 1.3 82.8 - - - +
381A THR* 1.3 75.0 + - - +
382A ARG* 4.1 2.7 - - - -
390A GLY* 3.4 2.1 - - - -
391A GLY 3.0 29.9 + - - +
393A GLN* 3.6 19.8 + - + -
411A PRO* 5.2 2.5 - - + -
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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