Contacts of the strand formed by residues 438 - 448 (chain A) in PDB entry 5LXX
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 GLU 438 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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367A ASP* 3.8 10.4 - - - +
417A VAL* 3.7 25.1 - - + +
418A LYS 3.7 2.0 - - - -
419A THR* 2.4 38.9 + - - +
436A GLY 3.3 7.1 + - - +
437A MET* 1.3 75.2 - - - +
439A CYS* 1.3 59.7 + - - +
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Residues in contact with CYS 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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363A SER* 3.2 46.2 - - - -
364A VAL* 3.8 7.0 - - - -
367A ASP* 3.7 12.8 - - - -
416A SER 4.5 0.2 - - - -
417A VAL* 3.4 2.9 - - - +
418A LYS* 2.8 39.4 + - + +
420A ILE* 3.9 22.2 - - + -
437A MET* 4.1 12.6 - - - -
438A GLU* 1.3 73.8 - - - +
440A ARG* 1.3 63.5 + - - +
441A GLY 3.7 4.0 + - - +
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Residues in contact with ARG 440 (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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363A SER 3.4 19.9 - - - +
366A TRP* 3.4 9.5 - - + +
367A ASP* 2.8 21.0 + - - +
371A VAL* 3.8 40.5 - - + +
414A PRO* 2.9 22.3 + - - +
415A ASP* 3.1 35.8 + - - +
416A SER 3.1 12.1 - - - +
417A VAL* 4.3 13.2 - - + +
438A GLU 4.1 0.6 + - - -
439A CYS* 1.3 72.7 - - - +
441A GLY* 1.3 58.0 + - - +
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Residues in contact with GLY 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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363A SER* 2.8 24.9 + - - -
366A TRP* 3.8 15.5 - - - -
412A TRP* 3.6 11.2 - - - -
413A ASP 3.3 13.9 - - - -
414A PRO 4.3 1.1 + - - -
416A SER* 2.9 13.0 + - - -
418A LYS* 6.0 0.9 - - - +
439A CYS 3.7 4.0 + - - +
440A ARG* 1.3 73.8 - - - +
442A SER* 1.3 62.9 + - - -
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Residues in contact with SER 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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363A SER* 4.0 2.2 - - - -
412A TRP* 3.6 11.9 - - - -
413A ASP* 2.8 33.4 + - - +
416A SER* 2.6 25.5 + - - -
418A LYS* 3.5 34.6 + - - -
441A GLY* 1.3 74.7 - - - -
443A PRO* 1.3 75.7 + - - +
444A LEU* 5.4 2.1 - - - +
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Residues in contact with PRO 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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98A ALA 3.2 27.4 - - - +
99A GLY* 3.7 18.2 - - - +
100A GLY* 3.8 2.2 - - - +
363A SER* 4.6 3.4 - - - +
410A VAL* 3.8 19.7 - - + -
411A ILE 3.8 5.4 - - - +
412A TRP* 3.7 13.9 - - + -
418A LYS* 4.6 7.4 + - - +
442A SER* 1.3 93.2 + - - +
444A LEU* 1.3 62.4 + - - +
446A VAL* 3.8 16.2 - - + -
454A LEU* 4.0 10.5 - - + +
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Residues in contact with LEU 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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63A ARG* 3.6 46.9 - - - +
411A ILE* 2.8 21.6 + - + +
413A ASP* 3.6 32.5 - - + +
418A LYS* 6.4 0.4 - - - +
442A SER* 3.6 2.2 + - - +
443A PRO* 1.3 77.7 - - - +
445A VAL* 1.3 69.2 + - + +
454A LEU* 3.9 6.9 - - - +
455A GLU* 3.8 14.4 - - - -
456A ASP 4.1 5.2 + - - -
457A GLY 5.1 1.7 + - - -
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Residues in contact with VAL 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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58A ILE* 4.1 31.4 - - + -
410A VAL* 3.3 9.5 - - - +
411A ILE* 2.9 50.6 + - + -
444A LEU* 1.3 88.1 - - + +
446A VAL* 1.3 66.8 + - - +
447A ILE* 4.2 17.7 - - + -
452A ILE* 4.5 5.8 - - + -
454A LEU 3.2 13.0 - - - +
455A GLU* 4.3 10.3 - - + +
456A ASP 5.5 0.4 - - - +
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Residues in contact with VAL 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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97A LEU* 3.4 29.2 - - + +
100A GLY* 4.2 6.7 - - - -
102A THR* 3.8 25.8 - - + -
409A LEU 3.6 4.3 - - - +
410A VAL* 4.3 4.7 - - + -
443A PRO* 3.8 13.7 - - + -
445A VAL* 1.3 79.2 - - - +
447A ILE* 1.3 65.6 + - - +
452A ILE* 3.7 3.8 - - - +
453A VAL* 2.9 41.8 + - + -
454A LEU* 3.0 35.1 + - + +
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Residues in contact with ILE 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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17A LEU* 3.9 21.1 - - + -
19A ILE* 3.6 31.0 - - + -
37A MET* 4.4 6.3 - - + -
58A ILE* 4.3 4.5 - - + -
102A THR* 3.7 4.9 - - - +
407A ALA 3.4 20.2 - - - +
408A ASP* 3.2 4.0 - - - -
409A LEU* 2.8 45.3 + - + +
410A VAL* 6.3 0.2 - - - -
411A ILE* 5.7 1.8 - - + -
445A VAL* 4.2 15.9 - - + -
446A VAL* 1.3 78.5 - - - +
448A SER* 1.3 61.2 + - - +
450A GLY* 3.6 24.2 - - - -
451A LYS 3.2 6.3 - - - +
452A ILE* 4.2 9.2 - - + -
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Residues in contact with SER 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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97A LEU* 4.0 22.7 - - - -
102A THR* 4.4 6.2 + - - -
132A CYS 4.3 4.0 + - - -
133A CYS* 4.2 20.4 - - - +
134A ASP* 4.7 0.9 + - - -
408A ASP* 3.6 7.0 + - - -
446A VAL 4.2 0.6 - - - -
447A ILE* 1.3 73.3 - - - +
449A GLN* 1.3 82.5 + - - +
450A GLY 3.1 0.2 - - - -
451A LYS* 2.9 23.7 + - - +
453A VAL* 4.2 14.1 - - - +
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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