Contacts of the helix formed by residues 514 - 531 (chain B) in PDB entry 5OF4
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 ILE 514 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A LEU* 3.2 34.7 - - + +
511B ARG* 5.6 4.3 - - + +
512B GLU 5.8 0.2 - - - -
513B ASP* 1.3 79.0 - - - +
515B ALA* 1.3 63.1 + - - +
516B VAL 3.1 2.0 - - - +
517B ILE* 3.2 18.7 + - + +
518B ARG* 2.9 29.9 + - - +
551B SER* 3.7 22.2 - - - +
555B GLN* 3.4 32.3 - - - +
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Residues in contact with ALA 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A LEU* 3.2 27.6 - - + +
311A LYS* 3.4 21.4 + - + +
358A ARG* 3.3 25.6 - - - +
513B ASP* 4.4 2.5 - - + +
514B ILE* 1.3 75.7 - - - +
516B VAL* 1.3 67.8 + - + +
518B ARG* 3.2 6.8 + - - +
519B ASN* 2.9 32.7 + - - +
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Residues in contact with VAL 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503B ALA* 3.2 40.8 - - + +
504B ILE* 4.2 7.4 - - - +
505B SER 4.6 6.5 - - - +
506B SER* 5.4 6.3 - - - -
508B PHE* 6.1 3.6 - - + -
513B ASP* 4.2 29.8 - - + +
515B ALA* 1.3 78.5 - - + +
517B ILE* 1.3 57.4 + - + +
519B ASN* 3.2 6.2 + - - +
520B TYR* 3.0 51.0 + - + -
544B TYR* 4.1 9.4 - - - +
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Residues in contact with ILE 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511B ARG* 5.5 2.9 - - + -
513B ASP 4.1 8.3 - - - +
514B ILE* 3.2 34.8 + - + +
516B VAL* 1.3 72.2 - - + +
518B ARG* 1.3 62.2 + - + +
520B TYR* 3.2 9.8 + - + +
521B GLY 2.9 23.0 + - - -
544B TYR* 3.5 34.8 - - + +
547B SER* 4.6 6.3 - - - +
548B THR* 4.0 27.6 - - + +
551B SER* 4.3 14.1 - - - +
552B TRP* 3.4 28.7 + - + +
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Residues in contact with ARG 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A LEU* 4.0 23.6 - - + +
311A LYS* 3.2 43.7 + - + +
312A PRO* 3.4 20.0 - - - +
313A THR* 4.1 15.9 + - + +
383A THR* 4.7 8.3 - - - +
514B ILE* 2.9 19.8 + - - +
515B ALA* 3.2 9.4 + - - +
517B ILE* 1.3 76.1 - - + +
519B ASN* 1.3 60.6 + - - +
521B GLY* 3.3 2.0 + - - +
522B ASN* 2.9 27.5 + - - +
551B SER* 6.5 0.2 - - - -
552B TRP* 6.4 0.2 - - + -
555B GLN* 2.9 50.6 + - - +
556B GLY* 5.3 3.8 - - - +
557B ILE* 4.3 17.0 - - + +
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Residues in contact with ASN 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A LYS* 3.4 26.3 + - - +
497B ARG* 4.3 12.0 - - + +
500B ASP* 3.2 40.4 + - - +
502B VAL* 6.2 0.6 - - - -
503B ALA 5.8 0.2 - - - +
504B ILE* 5.0 15.8 - - + +
515B ALA 2.9 21.8 + - - +
516B VAL* 3.6 8.5 - - - +
518B ARG* 1.3 73.6 - - - +
520B TYR* 1.3 68.2 + - - +
522B ASN* 3.3 12.2 + - - +
523B LEU* 3.0 23.9 + - - +
710B VAL* 4.9 4.0 - - - +
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Residues in contact with TYR 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B ILE* 2.5 43.0 + - + +
516B VAL* 3.0 49.9 + - + -
517B ILE* 3.2 15.2 + - + +
519B ASN* 1.3 78.1 - - - +
521B GLY* 1.3 57.1 + - - +
523B LEU* 3.2 15.6 + - + +
524B LEU* 2.9 27.5 + - - +
539B PHE* 5.2 5.4 - + - -
544B TYR* 4.0 18.0 - + - -
548B THR* 6.4 0.2 - - + -
552B TRP* 4.2 13.5 - + + -
621B PHE* 3.3 42.9 - + + -
622B GLY* 3.2 21.7 + - - -
680B ALA* 3.9 4.9 - - + -
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Residues in contact with GLY 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517B ILE 2.9 14.2 + - - -
518B ARG 3.3 3.5 + - - -
519B ASN 3.2 0.2 - - - -
520B TYR* 1.3 73.4 - - - +
522B ASN* 1.3 65.6 + - - +
524B LEU* 3.8 3.5 - - - +
525B LEU* 2.9 31.9 + - - +
552B TRP* 3.8 19.9 - - - +
557B ILE* 4.2 18.1 - - - +
561B ILE* 5.0 0.2 - - - +
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Residues in contact with ASN 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A THR* 5.6 4.2 - - + +
315A VAL* 3.7 26.5 - - + +
321A GLU* 5.3 0.4 + - - -
497B ARG* 4.3 25.5 - - - +
500B ASP* 4.5 5.9 + - - -
518B ARG 2.9 14.6 + - - +
519B ASN* 3.6 15.2 + - - +
520B TYR 3.3 0.2 - - - -
521B GLY* 1.3 74.4 - - - +
523B LEU* 1.3 62.7 + - - +
525B LEU* 3.3 12.2 - - + +
526B GLU* 3.1 51.0 + - - +
557B ILE* 5.5 0.4 - - - +
710B VAL* 4.5 5.7 - - - +
711B ASP* 4.8 2.6 + - - -
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Residues in contact with LEU 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495B ILE* 4.2 23.6 - - + -
504B ILE* 5.4 6.1 - - + -
519B ASN 3.0 12.0 + - - +
520B TYR* 3.2 41.3 + - + +
522B ASN* 1.3 75.8 - - - +
524B LEU* 1.3 59.9 + - - +
526B GLU* 3.8 1.0 - - - +
527B MET* 2.8 45.8 + - - +
619B ILE* 4.4 7.4 - - + -
621B PHE* 3.7 20.9 - - + -
680B ALA* 3.7 16.2 - - + -
710B VAL* 3.7 33.9 - - + +
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Residues in contact with LEU 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B TYR 2.9 15.7 + - - +
521B GLY* 3.2 7.6 + - - +
522B ASN 3.2 0.2 - - - -
523B LEU* 1.3 79.1 - - + +
525B LEU* 1.3 60.2 + - - +
527B MET* 3.3 6.0 + - + +
528B SER* 2.9 36.7 + - - +
535B ILE* 4.4 2.5 - - + -
537B ALA* 5.5 0.9 - - + -
552B TRP* 3.6 32.5 - - + -
561B ILE* 4.3 21.0 - - + +
567B LEU* 5.3 3.6 - - + -
595B ILE* 3.5 35.4 - - + -
597B LEU* 5.3 0.9 - - + -
619B ILE* 4.0 24.9 - - + -
621B PHE* 4.3 8.7 - - + -
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Residues in contact with LEU 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A THR* 4.7 8.7 - - + -
315A VAL* 4.6 16.4 - - + -
521B GLY 2.9 20.4 + - - +
522B ASN* 3.3 23.6 - - - +
524B LEU* 1.3 79.4 - - - +
526B GLU* 1.3 73.7 + - + +
528B SER* 3.5 4.2 + - - -
529B ALA* 3.0 26.2 + - - +
557B ILE* 5.0 6.3 - - + -
560B ASN* 3.4 40.4 - - - +
561B ILE* 4.4 11.4 - - + +
564B ASN* 4.5 6.9 + - - +
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Residues in contact with GLU 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A VAL* 3.3 19.2 - - - +
522B ASN* 3.1 30.7 + - - +
523B LEU 4.3 1.8 - - - +
525B LEU* 1.3 89.8 - - + +
527B MET* 1.3 56.5 + - - +
529B ALA* 3.2 10.2 + - + +
530B VAL* 3.1 33.1 + - - +
710B VAL* 3.4 18.7 - - - +
711B ASP* 2.8 28.2 - - - +
714B VAL* 3.9 21.2 - - + +
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Residues in contact with MET 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493B MET* 4.4 15.3 - - + -
495B ILE* 5.2 1.6 - - - -
523B LEU* 2.8 32.7 + - - +
524B LEU* 3.4 14.4 - - + +
526B GLU* 1.3 76.9 - - - +
528B SER* 1.3 51.6 + - - +
530B VAL* 3.2 2.2 + - + -
531B VAL* 2.7 55.3 + - + +
535B ILE* 4.0 10.3 - - + -
617B ALA* 5.6 1.1 - - + -
619B ILE* 3.8 22.9 - - + -
676B LEU* 3.6 31.6 - - + -
678B VAL* 4.7 7.9 - - + -
710B VAL* 6.3 1.1 - - - -
713B GLY 5.4 0.2 - - - +
714B VAL* 4.9 9.6 - - + +
717B ALA* 4.3 14.8 - - + -
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Residues in contact with SER 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B LEU* 2.9 23.1 + - - +
525B LEU* 4.0 6.1 - - - -
527B MET* 1.3 72.5 - - - +
529B ALA* 1.3 63.8 + - - +
531B VAL 3.6 4.2 - - - +
535B ILE* 3.7 18.3 - - - +
561B ILE* 4.5 16.1 - - - +
564B ASN* 4.6 16.9 + - - +
565B LYS* 3.4 36.7 + - - +
595B ILE* 4.7 5.2 - - - +
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Residues in contact with ALA 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B LEU* 3.0 14.8 + - + +
526B GLU* 3.2 15.9 + - + +
528B SER* 1.3 79.8 - - - +
530B VAL* 1.3 65.1 + - + +
564B ASN* 4.6 10.7 - - - +
174E LEU* 5.3 8.6 - - - +
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Residues in contact with VAL 530 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526B GLU 3.1 14.9 + - - +
527B MET* 4.0 2.7 - - + +
529B ALA* 1.3 83.7 - - + +
531B VAL* 1.3 71.0 - - + +
532B PRO* 3.6 7.1 - - - +
714B VAL* 3.7 28.9 - - + +
717B ALA* 4.7 4.9 - - + -
718B LYS* 3.7 38.6 - - + +
721B LEU* 3.7 23.1 - - + +
202E SER 5.3 5.5 - - - +
203E ALA* 4.4 11.8 - - - +
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Residues in contact with VAL 531 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B MET* 2.7 53.4 + - + +
528B SER* 3.6 4.0 - - - +
530B VAL* 1.3 82.2 - - + +
532B PRO* 1.4 81.9 - - + +
534B GLY 4.8 1.8 - - - +
535B ILE* 4.1 14.1 - - + +
565B LYS* 3.6 20.3 + - - -
616B ARG* 5.4 3.6 - - + -
617B ALA* 3.7 25.8 - - + -
676B LEU* 4.4 6.1 - - + -
717B ALA* 5.2 0.7 - - + -
721B LEU* 4.0 17.3 - - + -
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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
------------------------------------------------------------
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