Contacts of the strand formed by residues 439 - 453 (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 VAL 439 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361A PHE* 5.1 5.4 - - + -
435A LEU* 3.9 22.9 - - + -
437A ASP* 3.8 9.9 - - + +
438A PRO* 1.3 79.9 - - - +
440A GLU* 1.3 59.4 + - - +
441A VAL* 4.3 3.4 - - + -
513A VAL* 4.4 2.0 - - - -
514A PHE* 2.8 38.5 + - - -
520A ILE* 4.0 22.7 - - + -
571A ILE* 3.7 32.1 - - + -
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Residues in contact with GLU 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A VAL* 4.4 1.9 - - - +
346A ARG* 2.7 46.3 + - - -
438A PRO 4.2 0.6 - - - -
439A VAL* 1.3 73.4 - - - +
441A VAL* 1.3 64.3 + - - +
442A THR* 2.7 26.2 + - - +
512A ASN 3.5 4.9 - - - +
513A VAL* 3.8 26.7 - - + +
571A ILE* 3.4 9.8 - - - +
572A ILE* 3.0 56.6 + - + +
574A ARG* 5.4 1.6 - - - +
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Residues in contact with VAL 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A VAL* 4.3 3.6 - - + -
440A GLU* 1.3 76.0 - - - +
442A THR* 1.3 59.6 + - - +
445A VAL* 4.5 1.6 - - + -
464A LEU* 4.5 3.1 - - + -
510A THR* 3.7 17.3 - - + +
511A SER* 3.3 3.3 + - - -
512A ASN 2.8 36.6 + - - +
514A PHE* 3.5 28.5 - - + -
569A LEU* 4.2 22.7 - - + -
570A PRO* 3.3 34.5 - - + +
571A ILE* 3.9 17.9 - - + -
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Residues in contact with THR 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A LEU* 3.8 24.0 - - + -
346A ARG* 5.0 0.7 - - - +
351A TRP* 3.9 7.0 - - + -
353A LEU* 3.9 14.5 - - + +
356A THR* 4.3 4.5 + - - -
440A GLU* 2.7 30.5 + - - +
441A VAL* 1.3 75.6 + - - +
443A GLY* 1.3 60.7 + - - +
510A THR 3.3 2.9 - - - -
511A SER* 2.8 32.2 + - - +
570A PRO* 3.0 20.6 + - - +
572A ILE* 3.9 18.6 - - - +
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Residues in contact with GLY 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A TRP* 3.2 24.4 - - - -
352A PRO* 5.7 6.3 - - - -
353A LEU* 5.7 0.7 - - - -
356A THR* 5.6 2.2 - - - -
358A TYR* 5.8 0.2 - - - -
442A THR* 1.3 76.1 - - - +
444A THR* 1.3 66.4 + - - -
445A VAL* 3.7 4.0 + - - +
509A ALA* 3.2 0.3 - - - +
510A THR 3.0 30.3 + - - +
570A PRO* 3.5 7.9 - - - +
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Residues in contact with THR 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A LEU* 5.6 2.9 - - + -
351A TRP* 4.0 15.4 - - + +
352A PRO* 5.3 8.6 - - + +
358A TYR* 4.0 25.3 + - - -
443A GLY* 1.3 74.8 - - - -
445A VAL* 1.3 60.2 + - - +
508A LEU 3.3 13.0 - - - +
509A ALA* 3.8 7.2 - - + -
568A VAL 4.5 1.0 - - - +
570A PRO* 3.3 19.2 - - - +
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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
----------------------------------------------------------
441A VAL* 4.5 2.7 - - + -
443A GLY 3.8 10.1 - - - +
444A THR* 1.3 80.6 - - - +
446A SER* 1.3 66.6 + - - +
464A LEU* 4.6 2.2 - - + -
477A CYS* 3.9 28.7 - - - -
506A ASP* 4.0 2.4 - - - +
507A MET* 2.9 38.4 + - + +
508A LEU 2.9 8.2 + - - +
509A ALA* 4.5 1.8 - - - -
510A THR* 4.1 11.4 - - + -
567A ILE* 3.9 24.7 - - + -
568A VAL 3.9 12.6 - - - +
569A LEU* 4.2 3.1 - - + -
570A PRO* 3.8 14.4 - - + -
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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
----------------------------------------------------------
445A VAL* 1.3 78.4 - - - +
447A ALA* 1.3 64.5 + - - +
448A ARG* 5.2 4.5 + - - +
504A ALA* 6.0 2.9 - - - -
505A ILE 3.1 15.9 - - - -
506A ASP* 4.5 4.0 - - - -
507A MET* 4.0 6.5 - - - +
567A ILE* 3.5 5.0 - - - +
568A VAL* 2.8 44.9 + - - +
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Residues in contact with ALA 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A SER* 1.3 76.1 - - - +
448A ARG* 1.3 67.8 + - - +
449A LEU* 4.0 14.4 - - + -
462A ALA* 4.3 9.4 - - + -
503A VAL 3.7 0.2 - - - +
504A ALA* 3.2 6.1 - - - +
505A ILE* 2.9 40.5 + - + -
507A MET* 3.9 17.5 - - - -
522A VAL* 6.4 0.9 - - + -
566A HIS 3.5 10.1 - - - +
567A ILE* 4.1 6.5 - - + +
568A VAL* 4.5 0.4 - - - +
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Residues in contact with ARG 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A SER* 5.2 4.4 + - - +
447A ALA* 1.3 80.3 - - - +
449A LEU* 1.3 60.3 + - - +
450A PHE* 4.7 1.3 - - + -
502A GLU* 3.8 29.5 + - + +
503A VAL 3.3 7.0 - - - +
504A ALA* 4.0 20.8 - - - +
564A PRO 4.4 0.2 - - - +
565A SER* 3.3 5.5 - - - -
566A HIS* 2.9 61.8 + - + +
568A VAL* 5.0 7.0 - - + -
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Residues in contact with LEU 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A LEU* 4.0 29.2 - - + -
447A ALA* 4.5 11.0 - - + -
448A ARG* 1.3 81.9 - - - +
450A PHE* 1.3 64.5 + - - +
451A VAL* 3.8 13.7 - - + -
460A PHE* 5.0 3.1 - - + -
461A THR 4.8 0.2 - - - +
462A ALA* 5.0 0.9 - - + -
501A TYR 3.3 1.9 - - - +
502A GLU* 3.3 2.1 - - - -
503A VAL* 2.8 42.4 + - + +
505A ILE* 3.7 28.7 - - + -
524A VAL* 4.0 31.4 - - + -
557A ILE* 4.4 9.9 - - + -
565A SER* 3.6 6.7 - - - +
566A HIS 4.4 8.3 - - - +
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Residues in contact with PHE 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A ARG 4.8 2.0 - - - -
449A LEU* 1.3 73.8 - - - +
451A VAL* 1.3 62.7 + - - +
500A ILE* 4.0 13.0 - - + -
501A TYR 3.2 4.7 - - - -
502A GLU* 3.5 46.2 - - + -
557A ILE* 3.7 1.9 - - - +
558A HIS* 2.8 33.6 + - + +
562A GLU 4.4 3.8 - - - -
563A HIS* 3.6 43.7 - + + -
564A PRO* 3.5 37.9 - - + -
565A SER* 2.9 23.7 + - - +
566A HIS* 5.7 2.0 - + - -
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Residues in contact with VAL 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A LEU* 3.8 18.2 - - + +
450A PHE* 1.3 79.1 - - - +
452A SER* 1.3 62.7 + - - +
460A PHE* 3.5 39.9 - - + -
483A MET* 3.7 22.0 - - + -
499A GLU 3.6 0.5 - - - +
500A ILE* 3.3 3.1 - - - -
501A TYR* 2.8 39.6 + - - +
503A VAL* 4.2 9.2 - - + -
556A ARG 3.3 5.6 - - - +
557A ILE* 3.5 26.0 - - + -
558A HIS* 4.0 3.6 - - - -
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Residues in contact with SER 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A VAL* 1.3 80.2 - - - +
453A SER* 1.3 62.6 + - - +
460A PHE* 3.9 5.5 - - - -
483A MET* 6.3 0.2 - - - -
495A ILE* 5.8 0.7 - - - -
498A GLY* 4.0 17.4 - - - -
499A GLU 3.6 17.9 - - - -
500A ILE* 4.4 0.4 - - - -
501A TYR* 5.4 1.1 - - - -
554A VAL 4.8 0.2 - - - -
555A ASN* 3.5 1.9 - - - -
556A ARG* 2.9 41.6 + - - +
558A HIS* 2.8 28.4 + - - -
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Residues in contact with SER 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A SER* 1.3 75.7 - - - +
454A SER* 1.3 60.3 + - - +
455A ALA* 3.0 28.9 + - - +
458A THR* 3.8 18.0 - - - +
460A PHE* 4.9 0.9 - - - -
495A ILE* 4.1 12.9 - - - +
496A GLU 4.5 0.8 + - - +
497A ALA* 3.2 7.4 - - - -
498A GLY* 2.8 25.8 + - - +
499A GLU 4.7 1.0 + - - -
553A ALA* 4.0 0.5 - - - +
554A VAL 3.6 3.1 - - - -
555A ASN* 2.6 27.9 + - - +
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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
------------------------------------------------------------
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