Contacts of the helix formed by residues 521 - 538 (chain B) in PDB entry 3F7F
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 SER 521 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B LEU* 1.3 77.0 - - - +
522B ASN* 1.3 68.0 + - - +
523B ASP* 3.7 7.1 + - - +
524B VAL* 3.1 29.1 + - - +
525B LEU* 2.9 26.1 + - - +
561B GLN 5.6 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 522 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B ASP* 3.2 49.6 + - - +
395B LEU* 4.5 3.0 - - - +
396B ASP 3.6 25.5 + - - +
397B ILE* 4.8 7.5 - - + +
521B SER* 1.3 74.2 - - - +
523B ASP* 1.3 62.9 + - - +
525B LEU* 3.2 10.6 + - - +
526B ARG* 2.8 44.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 523 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521B SER* 3.3 7.4 + - - +
522B ASN* 1.3 81.4 - - - +
524B VAL* 1.3 62.8 + - + +
526B ARG* 3.9 14.3 - - - +
527B SER* 3.2 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 524 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B LEU* 4.5 9.9 - - + -
521B SER* 3.1 28.6 + - - +
523B ASP* 1.3 76.7 - - + +
525B LEU* 1.3 66.1 + - - +
527B SER* 2.6 23.4 + - - -
528B ILE* 3.1 23.3 + - + +
557B CYS 3.7 19.5 - - - +
558B LEU* 4.1 10.5 - - + -
561B GLN* 3.7 36.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 525 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B ILE* 3.5 29.2 - - + -
517B ALA* 4.0 22.7 - - + +
518B SER* 5.9 0.2 - - - -
520B LEU* 4.0 28.9 - - + +
521B SER 2.9 22.6 + - - +
522B ASN* 3.8 7.9 - - - +
524B VAL* 1.3 75.9 - - - +
526B ARG* 1.3 56.3 + - - +
528B ILE* 3.1 11.5 + - + +
529B SER* 2.9 28.4 + - - -
631B LEU* 4.2 20.0 - - + +
632B GLN* 6.3 0.9 - - + -
635B LEU* 4.9 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 526 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B ASP 3.3 10.5 + - - -
397B ILE* 3.0 60.1 + - + +
398B VAL 3.8 2.2 + - - -
399B THR 2.5 31.9 + - - -
400B LYS* 4.3 3.2 - - - +
401B THR* 3.7 25.9 + - - +
522B ASN* 2.8 39.3 + - - +
523B ASP* 3.9 15.0 - - - +
525B LEU* 1.3 72.9 - - - +
527B SER* 1.3 59.2 + - - +
529B SER* 3.2 2.8 + - - -
530B LYS* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 527 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B ASP 3.2 11.9 + - - -
524B VAL* 2.6 24.0 + - - -
526B ARG* 1.3 79.9 - - - +
528B ILE* 1.3 57.1 + - - +
530B LYS* 3.7 7.3 + - - +
531B LYS* 3.2 30.0 + - - +
556B ASN 5.7 0.4 - - - -
557B CYS* 3.4 25.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 528 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B LEU* 4.8 3.8 - - + -
524B VAL* 3.1 20.4 + - + +
525B LEU* 3.4 14.4 - - + +
526B ARG 3.1 0.2 - - - -
527B SER* 1.3 76.4 + - - +
529B SER* 1.3 64.8 + - - +
531B LYS* 3.1 6.3 + - - +
532B PHE* 3.0 52.3 + - + -
553B ILE* 4.5 6.7 - - + -
557B CYS* 3.6 21.1 - - + -
558B LEU* 3.3 42.2 - - + -
631B LEU* 4.3 7.2 - - + -
635B LEU* 4.1 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 529 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B ILE* 4.8 1.8 - - - -
525B LEU 2.9 15.0 + - - -
526B ARG* 3.6 8.3 - - - -
528B ILE* 1.3 76.6 - - - +
530B LYS* 1.3 63.9 + - - +
532B PHE 3.0 10.4 + - - -
533B LEU* 3.0 13.0 + - - +
627B TYR* 2.5 30.7 + - - -
631B LEU* 3.8 15.7 - - - -
658B HIS* 2.8 29.2 + - - -
662B PHE* 4.1 9.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 530 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526B ARG 2.9 16.6 + - - +
527B SER* 3.7 9.2 - - - +
529B SER* 1.3 78.4 - - - +
531B LYS* 1.3 55.7 + - + +
533B LEU* 3.1 23.6 + - + +
534B ASP* 3.0 56.8 + - - +
539B GLU* 3.3 25.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 531 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B SER 3.2 14.7 + - - +
528B ILE 3.1 10.4 + - - +
530B LYS* 1.3 77.9 - - + +
532B PHE* 1.3 67.0 + - - +
534B ASP* 3.1 27.0 + - - +
535B ILE* 3.1 11.4 + - - +
540B LEU* 3.5 28.4 - - + +
552B ASP* 3.3 25.7 + - - -
553B ILE* 3.3 27.8 - - + +
556B ASN* 4.0 19.6 - - - +
557B CYS* 3.8 12.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 532 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528B ILE* 3.0 40.3 + - + -
529B SER 3.0 6.7 + - - +
531B LYS* 1.3 74.8 - - - +
533B LEU* 1.3 61.0 + - - +
535B ILE* 3.3 20.5 + - + +
536B ILE* 3.5 11.4 + - - +
550B PHE* 4.8 3.8 - + - -
553B ILE* 3.4 27.8 - - + -
631B LEU* 3.7 24.9 - - + -
634B LEU* 3.5 39.0 - - + -
635B LEU* 4.3 1.6 - - - -
638B VAL* 3.8 23.8 - - + -
655B LEU* 3.7 24.3 - - + +
658B HIS* 3.6 16.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 533 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529B SER 3.0 18.3 + - - +
530B LYS* 3.1 24.0 + - + +
532B PHE* 1.3 74.5 - - - +
534B ASP* 1.3 61.8 + - - +
536B ILE* 3.1 3.7 + - - +
537B THR* 2.8 35.1 + - + +
658B HIS* 4.0 10.1 - - + -
659B TYR* 3.5 45.5 - - + -
662B PHE* 3.5 45.8 - - + -
729B ILE* 3.8 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 534 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530B LYS* 3.0 49.8 + - - +
531B LYS* 3.1 29.5 + - - +
533B LEU* 1.3 74.5 - - - +
535B ILE* 1.3 58.3 + - - +
537B THR* 3.1 5.9 + - - -
538B GLY* 2.7 28.2 + - - -
539B GLU* 3.0 38.7 + - + +
540B LEU* 3.3 17.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 535 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531B LYS 3.1 11.7 + - - +
532B PHE* 3.4 14.1 - - + +
533B LEU 3.2 0.4 - - - -
534B ASP* 1.3 78.4 - - - +
536B ILE* 1.3 65.7 + - + +
538B GLY* 3.6 6.6 + - - -
540B LEU* 3.7 21.8 - - + +
549B LYS* 4.0 44.2 + - + +
550B PHE* 4.2 9.6 - - + -
553B ILE* 4.2 18.6 - - + -
655B LEU* 4.1 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 536 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B PHE 3.5 9.6 + - - +
533B LEU 3.1 7.6 + - - +
535B ILE* 1.3 83.4 - - + +
537B THR* 1.3 60.1 + - - +
538B GLY 3.6 0.2 + - - -
652B SER 5.5 1.1 - - - +
655B LEU* 3.6 40.4 - - + +
656B ASP* 4.4 11.0 - - + +
659B TYR* 3.6 35.7 - - + -
714B ILE* 4.1 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 537 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681A LYS* 5.8 1.6 + - - -
533B LEU* 2.8 26.3 + - + +
534B ASP* 3.1 18.4 + - - -
536B ILE* 1.3 75.6 - - - +
538B GLY* 1.3 59.7 + - - +
539B GLU* 3.5 12.5 + - - +
659B TYR* 3.9 19.1 - - + +
725B ARG* 3.5 45.7 + - - +
729B ILE* 5.1 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 538 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681A LYS* 5.4 7.2 + - - -
534B ASP 2.7 14.0 + - - -
535B ILE 3.6 3.6 + - - -
536B ILE 3.3 3.2 - - - -
537B THR* 1.3 75.8 - - - +
539B GLU* 1.3 59.7 + - - -
540B LEU 2.8 14.1 + - - -
541B PRO* 3.3 16.3 - - - +
542B ASP* 5.2 4.7 - - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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