Contacts of the strand formed by residues 501 - 514 (chain A) in PDB entry 1L7R
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 TYR 501 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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449A LEU 3.3 2.1 - - - +
450A PHE* 3.2 4.5 - - - -
451A VAL* 2.8 35.7 + - - +
452A SER* 5.4 1.1 - - - -
483A MET* 4.0 23.1 - - + -
486A ARG* 3.9 26.6 + - - -
494A LEU 4.8 0.5 + - - -
495A ILE* 3.4 30.8 - - + -
496A GLU* 2.8 28.8 + - - +
499A GLU* 3.3 63.3 + - + -
500A ILE* 1.3 76.1 - - - +
502A GLU* 1.3 60.5 + - - +
503A VAL* 3.7 6.7 + - + -
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Residues in contact with GLU 502 (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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448A ARG* 3.8 34.3 + - + +
449A LEU 3.3 7.6 - - - +
450A PHE* 3.5 44.2 - - + +
501A TYR* 1.3 73.3 - - - +
503A VAL* 1.3 66.0 + - - +
566A HIS* 5.4 2.6 - - - -
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Residues in contact with VAL 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A ALA 3.7 0.2 - - - +
448A ARG* 3.3 6.7 - - - -
449A LEU* 2.8 46.2 + - + +
451A VAL* 4.2 18.2 - - + -
460A PHE* 5.2 1.3 - - + -
481A VAL* 4.1 21.5 - - + -
483A MET* 3.6 32.3 - - + -
486A ARG* 3.9 22.0 - - + -
501A TYR* 4.1 9.6 - - + +
502A GLU* 1.3 80.8 - - - +
504A ALA* 1.3 63.0 + - - +
505A ILE* 4.9 3.8 - - + +
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Residues in contact with ALA 504 (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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446A SER* 6.0 2.7 - - - -
447A ALA 3.2 9.0 - - - +
448A ARG* 4.0 26.2 - - - +
481A VAL* 3.7 18.4 - - - +
486A ARG 5.4 6.3 + - - +
503A VAL* 1.3 74.8 - - - +
505A ILE* 1.3 66.3 + - - +
506A ASP 4.1 0.8 + - - -
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Residues in contact with ILE 505 (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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446A SER* 3.1 8.4 - - - -
447A ALA* 2.9 43.0 + - + +
449A LEU* 3.7 30.7 - - + -
460A PHE* 3.5 25.8 - - + +
461A THR 4.1 0.4 - - - -
462A ALA* 4.0 13.0 - - + -
479A GLY* 3.4 37.5 - - - +
480A ILE* 3.5 4.7 - - - +
481A VAL* 3.7 19.5 - - + -
503A VAL* 4.9 4.5 - - + +
504A ALA* 1.3 79.2 - - - +
506A ASP* 1.3 60.6 + - - +
507A MET* 3.3 9.7 + - + +
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Residues in contact with ASP 506 (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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148A ARG* 3.8 10.9 + - - -
154A PRO* 3.5 39.8 - - + +
155A GLY 5.5 0.7 - - - +
267A ARG* 5.7 0.2 + - - -
445A VAL 4.1 4.8 - - - +
446A SER* 4.5 4.7 - - - -
478A ASP 4.1 0.2 - - - +
479A GLY* 3.2 17.8 - - - -
480A ILE 4.2 5.0 + - - +
504A ALA 4.1 1.4 - - - -
505A ILE* 1.3 69.7 - - - +
507A MET* 1.3 59.0 + - - +
508A LEU* 2.9 29.7 + - - +
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Residues in contact with MET 507 (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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445A VAL* 2.9 26.8 + - + +
446A SER 4.0 2.9 - - - -
447A ALA* 3.9 13.9 - - - -
462A ALA* 3.5 34.5 - - + +
463A LYS 3.8 1.1 - - - -
464A LEU* 3.5 28.5 - - + +
477A CYS* 3.2 23.7 - - - +
478A ASP* 3.6 11.7 - - - +
479A GLY 3.8 11.4 - - - +
505A ILE* 3.7 13.9 - - + +
506A ASP* 1.3 72.1 - - - +
508A LEU* 1.3 70.9 + - - +
509A ALA 3.2 2.4 + - - -
522A VAL* 5.3 0.9 - - + -
567A ILE* 3.7 29.4 - - + -
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Residues in contact with LEU 508 (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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154A PRO* 4.5 17.3 - - + -
260A GLY 5.3 5.4 - - - +
262A VAL* 3.7 30.3 - - + -
263A GLY* 4.0 22.4 - - - +
405A THR* 4.3 19.7 - - + +
444A THR* 3.3 9.2 - - - +
445A VAL 2.9 22.3 + - - +
477A CYS* 5.0 2.5 - - + -
478A ASP 4.1 12.8 - - - +
506A ASP* 2.9 29.2 + - - +
507A MET* 1.3 78.1 - - - +
509A ALA* 1.3 68.3 + - - +
532A TYR* 5.7 4.5 - - - +
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Residues in contact with ALA 509 (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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257A TRP* 3.9 17.6 - - + +
262A VAL* 5.3 4.1 - - + +
266A LEU* 3.6 31.2 - - + +
351A TRP* 3.9 5.4 - - + -
443A GLY 3.2 18.4 - - - +
444A THR* 3.8 7.4 - - + -
445A VAL* 4.3 2.5 - - - +
476A LEU 4.8 0.2 - - - +
477A CYS* 3.6 12.6 - - - +
507A MET 3.2 2.9 + - - -
508A LEU* 1.3 85.8 - - - +
510A THR* 1.3 67.6 + - - +
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Residues in contact with THR 510 (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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257A TRP* 3.6 17.6 - - - +
340A MET* 3.4 19.9 - - - +
441A VAL* 3.9 20.6 - - + +
442A THR* 3.3 1.6 - - - -
443A GLY 3.0 27.7 + - - +
445A VAL* 4.1 11.2 - - + -
464A LEU* 4.3 8.3 - - + -
476A LEU* 3.9 16.0 + - + +
477A CYS* 4.1 21.3 - - - -
509A ALA* 1.3 79.9 - - - +
511A SER* 1.3 68.4 + - - +
512A ASN* 4.6 4.0 - - + +
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Residues in contact with SER 511 (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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257A TRP* 3.3 33.4 - - - -
337A LEU* 4.7 1.9 - - - +
338A PHE 4.0 2.9 - - - -
339A VAL* 3.5 24.1 - - - +
340A MET* 3.0 29.8 + - - +
441A VAL 3.3 4.5 - - - -
442A THR* 2.8 25.6 + - - +
510A THR* 1.3 77.9 + - - +
512A ASN* 1.3 60.0 + - - +
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Residues in contact with ASN 512 (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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297A ARG* 4.8 2.3 + - - -
340A MET* 3.3 28.9 - - - +
341A GLY* 3.4 5.4 + - - -
439A VAL 3.7 1.4 - - - +
440A GLU* 3.5 1.1 - - - -
441A VAL* 2.8 39.2 + - - +
442A THR* 4.0 0.8 + - - -
466A ASP* 3.0 26.8 + - - +
476A LEU* 3.7 32.3 - - + +
510A THR* 4.4 2.7 - - + +
511A SER* 1.3 76.9 + - - +
513A VAL* 1.3 65.8 + - - +
514A PHE* 3.6 31.1 + - + -
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Residues in contact with VAL 513 (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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339A VAL* 3.7 24.5 - - + -
340A MET 2.8 13.8 + - - +
341A GLY* 3.4 17.3 - - - -
342A ILE* 4.0 25.1 - - + +
438A PRO* 3.9 20.6 - - + -
439A VAL 3.5 8.1 - - - +
440A GLU* 3.8 21.5 - - + +
466A ASP* 4.2 2.1 - - - +
512A ASN* 1.3 76.2 + - - +
514A PHE* 1.3 58.7 + - - +
515A LEU* 3.2 28.9 + - + +
518A HIS* 5.9 0.3 - - - -
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Residues in contact with PHE 514 (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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435A LEU* 3.5 21.9 - - + +
438A PRO* 3.3 4.7 - - - +
439A VAL* 2.8 41.5 + - + +
441A VAL* 3.5 31.2 - - + -
464A LEU* 4.2 12.6 - - + -
465A VAL 3.6 22.2 - - - -
466A ASP* 3.6 28.9 - - + -
476A LEU* 3.3 22.7 - - + -
512A ASN* 3.6 13.9 - - + +
513A VAL* 1.3 69.0 - - - +
515A LEU* 1.3 62.3 + - - +
518A HIS* 4.7 3.1 - - + -
519A ARG 3.8 7.9 - - - -
520A ILE* 3.6 31.4 - - + -
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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