Contacts of the strand formed by residues 437 - 451 (chain A) in PDB entry 3L81
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 HIS 437 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A ASN 2.9 9.0 + - - +
186A GLU* 3.4 9.0 - - + +
187A VAL* 2.9 26.2 + - - +
436A PRO* 1.3 73.3 - - - +
438A LYS* 1.3 68.9 + - - +
439A TRP* 3.3 47.4 - + + -
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Residues in contact with LYS 438 (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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187A VAL* 3.4 11.4 - - + +
424A LEU* 2.7 52.1 + - + +
425A ARG* 4.4 5.2 - - - +
426A LEU* 4.1 24.8 - - + +
436A PRO* 3.9 12.3 + - - +
437A HIS* 1.3 86.7 + - - +
439A TRP* 1.3 68.9 + - - +
440A VAL* 4.1 5.1 + - + -
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Residues in contact with TRP 439 (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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186A GLU* 3.4 34.1 - - + -
187A VAL 2.9 11.5 + - - +
188A PHE* 3.5 41.2 - + + +
189A LEU 2.8 32.6 + - - +
424A LEU* 5.1 0.5 - - - +
437A HIS* 3.3 37.7 + + + -
438A LYS* 1.3 78.1 - - - +
440A VAL* 1.3 57.9 + - - +
441A ARG* 4.1 23.2 + - + +
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Residues in contact with VAL 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A LEU* 3.3 11.9 - - + +
191A VAL* 5.9 0.2 - - + -
421A VAL* 4.1 24.5 - - + +
424A LEU* 3.9 33.7 - - + +
438A LYS* 4.1 5.1 - - + -
439A TRP* 1.3 76.5 - - - +
441A ARG* 1.3 65.8 + - - +
442A HIS* 3.9 24.5 + - + -
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Residues in contact with ARG 441 (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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188A PHE* 3.9 32.8 - - - +
189A LEU 3.0 7.1 + - - +
190A ASP* 2.8 45.8 + - - +
191A VAL* 2.9 26.4 + - - +
439A TRP* 4.6 19.4 + - + +
440A VAL* 1.3 84.0 - - - +
442A HIS* 1.3 68.7 + - - +
443A LEU* 6.1 1.1 - - + -
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Residues in contact with HIS 442 (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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191A VAL* 3.4 28.6 - - + +
413A ARG* 2.8 32.7 + - - +
414A HIS 3.2 12.7 + - - +
415A THR* 3.8 23.3 - - + -
419A LEU 4.1 0.4 - - - -
420A GLN* 3.5 23.5 + - + +
421A VAL 3.0 31.8 + - - -
440A VAL* 3.9 25.8 + - + +
441A ARG* 1.3 75.7 - - - +
443A LEU* 1.3 62.1 + - - +
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Residues in contact with LEU 443 (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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190A ASP* 6.0 1.8 - - - +
191A VAL 2.9 10.1 + - - +
192A VAL* 3.3 26.8 - - + +
193A GLU* 2.9 24.4 + - - +
410A GLU* 4.1 23.1 - - + +
411A LEU 3.5 24.9 - - - +
412A PRO* 4.0 9.6 - - + -
414A HIS 3.3 7.4 + - - +
415A THR* 4.8 0.5 - - - +
441A ARG* 5.7 1.6 - - + -
442A HIS* 1.3 75.2 - - - +
444A SER* 1.3 72.4 + - - +
445A HIS* 4.8 9.4 - - + -
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Residues in contact with SER 444 (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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193A GLU* 3.2 12.3 - - - +
195A LEU* 5.6 0.2 - - - -
409A PHE* 6.0 0.2 - - - -
410A GLU* 3.5 0.7 - - - -
411A LEU* 2.7 44.3 + - - -
414A HIS* 3.1 25.6 + - - -
415A THR* 3.3 1.9 - - - -
416A CYS* 3.2 42.1 + - - -
443A LEU* 1.3 76.7 + - - +
445A HIS* 1.3 62.9 + - - +
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Residues in contact with HIS 445 (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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2A GOL 2.6 30.4 + - - +
192A VAL* 3.9 24.9 - - + +
193A GLU 2.9 18.4 + - - -
194A ARG* 3.4 52.4 - - + +
195A LEU* 2.9 26.5 + - - +
409A PHE* 3.2 17.3 - - - +
410A GLU* 4.2 9.0 - - + -
443A LEU* 4.8 8.5 - - + -
444A SER* 1.3 78.4 - - - +
446A SER* 1.3 61.2 + - - +
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Residues in contact with SER 446 (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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2A GOL 2.9 22.8 + - - -
194A ARG* 5.1 1.8 - - - +
195A LEU* 2.6 28.2 + - - -
407A LEU 4.5 0.2 - - - -
408A SER* 3.1 1.5 - - - -
409A PHE* 3.0 52.7 + - - -
445A HIS* 1.3 73.9 - - - +
447A ASP* 1.3 59.5 + - - +
448A ALA 3.1 11.3 + - - -
449A TYR* 3.4 13.9 + - - +
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Residues in contact with ASP 447 (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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2A GOL 3.7 16.7 + - - +
194A ARG* 2.9 28.1 + - - +
195A LEU 4.5 0.8 + - - -
196A SER* 5.4 0.7 + - - -
406A SER* 3.9 9.5 + - - -
407A LEU 3.9 6.7 - - - -
408A SER* 3.8 11.4 - - - -
446A SER* 1.3 75.4 - - - +
448A ALA* 1.3 65.5 + - - +
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Residues in contact with ALA 448 (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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195A LEU 4.6 0.2 + - - -
196A SER* 3.4 19.4 - - - +
197A VAL 3.1 24.3 + - - +
406A SER* 4.2 6.3 - - - -
446A SER* 3.1 6.4 + - - -
447A ASP* 1.3 88.3 - - - +
449A TYR* 1.3 60.9 + - - +
450A VAL* 3.5 10.5 - - + +
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Residues in contact with TYR 449 (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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195A LEU* 3.9 15.0 - - + -
197A VAL* 3.9 23.6 - - + +
199A ILE* 4.0 13.4 - - + +
294A LEU* 3.3 16.0 - - + +
295A PRO* 3.9 19.3 - - + -
296A PHE* 2.7 52.3 + - + -
405A ALA 3.8 0.5 - - - +
406A SER* 3.4 2.0 + - - -
407A LEU* 2.8 55.2 + - + +
409A PHE* 3.7 18.2 - + + -
446A SER* 3.6 9.0 - - - +
448A ALA* 1.3 74.4 - - - +
450A VAL* 1.3 60.0 + - - +
451A ILE* 3.9 19.0 + - + +
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Residues in contact with VAL 450 (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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197A VAL* 2.9 16.3 + - - +
198A LEU* 3.4 22.0 - - + -
199A ILE* 2.8 26.4 + - - +
404A PRO* 3.7 25.8 - - + -
405A ALA 3.3 9.2 - - - +
406A SER* 4.0 14.1 - - - +
448A ALA* 3.9 19.1 - - + +
449A TYR* 1.3 75.3 - - - +
451A ILE* 1.3 66.4 + - - +
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Residues in contact with ILE 451 (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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199A ILE* 3.6 31.6 - - + -
200A ALA 4.8 1.8 - - - +
296A PHE 4.7 1.6 - - - +
297A ARG 4.9 0.4 - - - -
298A LEU* 3.7 54.3 - - + +
300A PRO* 6.0 1.3 - - + -
404A PRO* 3.5 2.9 - - - +
405A ALA* 2.8 40.3 + - + +
407A LEU* 4.4 13.5 - - + -
449A TYR* 3.9 29.6 - - + +
450A VAL* 1.3 79.5 - - - +
452A ARG* 1.3 73.8 + - - +
453A ILE* 4.0 0.5 - - - +
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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