Contacts of the helix formed by residues 554 - 568 (chain A) in PDB entry 3M62
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 ARG 554 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A LEU* 2.9 31.1 + - - +
328A ASP* 4.2 5.3 - - - +
329A ILE* 3.7 33.2 - - + +
331A TYR* 2.9 28.7 + - - -
471A ASP* 3.9 42.0 + - - +
474A CYS* 3.3 24.5 - - + +
475A GLY* 3.3 15.2 - - - +
552A ASN* 2.8 17.3 + - - +
553A PRO* 1.3 75.8 - - + +
555A LEU* 1.3 64.2 + - - +
556A GLY* 3.1 3.6 - - - -
557A SER* 2.9 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 555 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A PHE* 4.2 13.0 - - + -
474A CYS* 4.1 7.2 - - - -
549A ILE* 3.9 30.1 - - + +
551A ARG* 5.5 1.6 - - - +
552A ASN* 2.9 21.4 + - + +
553A PRO 3.3 0.4 - - - -
554A ARG* 1.3 76.9 - - - +
556A GLY* 1.3 62.6 + - - +
557A SER 3.0 1.6 + - - -
558A PHE* 3.1 17.8 + - + +
559A VAL* 3.3 21.0 + - + -
599A PHE* 3.8 34.8 - - + +
600A MET* 3.9 18.4 - - + -
603A ILE* 3.8 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 556 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A PRO 4.5 4.1 + - - -
554A ARG 3.1 2.2 + - - -
555A LEU* 1.3 76.7 - - - +
557A SER* 1.3 56.0 + - - +
559A VAL* 3.4 2.0 + - - +
560A GLU* 2.9 40.3 + - - +
603A ILE* 3.3 29.2 - - - +
607A ASP* 4.2 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 557 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A TYR* 3.7 9.7 + - - -
474A CYS* 3.4 25.1 - - - +
477A SER* 3.6 9.6 - - - -
478A THR* 3.5 17.2 + - - -
481A ILE* 4.1 2.3 - - - +
554A ARG* 2.9 18.0 + - - +
556A GLY* 1.3 74.3 - - - +
558A PHE* 1.3 57.9 + - - +
560A GLU* 3.1 18.1 + - - +
561A PHE* 3.0 22.5 + - - +
962A 1PE 5.3 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 558 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A PHE* 4.3 23.3 - + + -
473A ILE* 3.8 10.3 - - + -
474A CYS* 4.4 6.5 - - - -
477A SER* 3.2 23.7 - - - +
534A PRO* 3.9 20.2 - - + -
535A VAL* 4.3 19.5 - - + -
538A SER* 3.7 15.3 - - - -
554A ARG 4.2 0.4 + - - -
555A LEU* 3.1 15.0 + - + +
557A SER* 1.3 78.1 - - - +
559A VAL* 1.3 61.0 + - + +
561A PHE* 3.2 15.1 + + - +
562A THR* 2.8 45.2 + - - -
581A LEU* 4.6 4.3 - - + -
584A LEU* 2.9 37.2 - - + -
600A MET* 5.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 559 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A LEU* 3.3 29.9 + - + +
556A GLY 3.9 5.8 - - - +
558A PHE* 1.3 76.7 - - + +
560A GLU* 1.3 55.5 + - - +
562A THR* 3.3 6.8 + - - -
563A THR* 2.7 46.8 + - - +
585A LEU* 4.2 6.7 - - + -
600A MET* 3.9 25.6 - - + -
603A ILE* 4.1 15.9 - - + -
604A PHE* 3.7 26.2 - - + -
610A VAL* 4.0 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 560 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A THR* 5.2 0.5 + - - -
481A ILE* 3.8 10.2 - - + +
490A PHE* 3.5 21.5 - - - -
556A GLY* 2.9 18.1 + - - +
557A SER* 3.1 20.1 + - - +
559A VAL* 1.3 76.2 - - - +
561A PHE* 1.3 63.5 + - - +
563A THR* 3.2 4.2 + - - -
564A MET* 3.0 23.0 + - - +
607A ASP* 2.4 38.8 - - - +
609A LEU* 3.9 20.3 - - + +
610A VAL* 4.0 7.4 - - + -
962A 1PE 3.6 26.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 561 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A SER* 3.8 20.9 - - - -
480A LEU* 3.6 37.9 - - + -
481A ILE* 3.5 11.6 - - + +
523A PHE* 4.3 9.0 - + - -
531A VAL* 3.7 39.7 - - + -
534A PRO* 6.4 1.1 - - + -
557A SER 3.0 9.6 + - - +
558A PHE* 3.2 20.2 + + - +
560A GLU* 1.3 79.1 - - - +
562A THR* 1.3 70.8 + - - +
564A MET* 3.3 28.3 + - + +
565A VAL* 3.0 43.7 + - + +
581A LEU* 5.2 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 562 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558A PHE* 2.8 34.7 + - - -
559A VAL* 3.5 8.6 - - - -
560A GLU 3.2 0.2 - - - -
561A PHE* 1.3 80.4 - - - +
563A THR* 1.3 57.8 + - - +
565A VAL* 3.2 4.8 + - - +
566A LEU* 2.9 32.7 + - + +
581A LEU* 3.6 42.6 - - + +
584A LEU* 5.1 1.4 - - + +
585A LEU* 3.8 31.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 563 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A LEU* 6.1 0.4 - - + -
559A VAL* 2.7 28.9 + - - +
560A GLU 3.7 3.1 - - - -
562A THR* 1.3 74.7 - - - +
564A MET* 1.3 56.1 + - - +
566A LEU* 3.2 8.3 + - - +
567A ARG* 2.7 38.2 + - - +
585A LEU* 4.8 1.7 - - - +
609A LEU* 4.7 2.0 - - - +
610A VAL* 3.9 23.3 - - - +
613A ASN* 4.0 13.7 - - + -
614A LEU* 3.7 47.4 - - + +
617A ALA* 4.4 2.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 564 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A ILE* 3.7 21.5 - - + -
484A VAL* 3.8 42.2 - - + -
495A ILE* 4.2 13.7 - - - -
497A LEU* 4.0 31.9 - - + +
523A PHE* 5.3 0.2 - - + -
560A GLU 3.0 12.5 + - - +
561A PHE* 3.4 39.3 - - + +
563A THR* 1.3 75.7 - - - +
565A VAL* 1.3 56.0 + - + +
567A ARG* 3.1 1.7 + - - -
568A CYS* 3.0 32.7 + - - +
571A LEU* 3.6 15.9 - - + -
609A LEU* 5.3 2.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 565 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A PHE* 5.2 0.7 - - + -
531A VAL* 5.9 0.2 - - + -
561A PHE* 3.0 52.6 + - + +
562A THR* 3.6 3.8 - - - +
564A MET* 1.3 75.9 - - + +
566A LEU* 1.3 61.7 + - - +
568A CYS 3.4 17.7 - - - +
571A LEU* 4.1 16.3 - - + +
572A VAL* 3.8 29.6 + - + +
578A LYS* 4.0 19.9 + - + +
581A LEU* 3.5 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 566 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562A THR* 2.9 26.8 + - + +
563A THR* 3.8 5.2 - - - +
565A VAL* 1.3 76.4 - - + +
567A ARG* 1.3 62.1 + - - +
568A CYS 4.9 0.7 - - - -
569A PRO* 5.0 3.2 - - - +
578A LYS* 3.9 42.1 - - + +
581A LEU* 4.5 5.2 - - + -
582A VAL* 4.1 17.7 - - + -
585A LEU* 3.8 29.4 - - + -
614A LEU* 5.1 2.0 - - + -
617A ALA* 3.7 26.8 - - + +
618A LEU* 4.7 7.0 - - + -
620A ASP* 5.3 3.8 - - - +
621A PHE* 4.5 22.9 + - + +
624A ILE* 6.0 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 567 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A LEU* 4.4 6.1 - - + -
498A PRO* 3.8 23.4 - - + +
502A ASP* 2.6 45.6 + - - -
563A THR 2.7 22.7 + - - +
564A MET* 3.1 6.5 + - - +
566A LEU* 1.3 73.9 - - - +
568A CYS* 1.3 68.4 + - - +
569A PRO* 3.6 9.1 - - - +
612A LYS 5.4 0.6 + - - -
613A ASN* 3.4 47.3 + - + +
616A TYR* 3.3 39.8 - - - +
617A ALA* 3.7 9.6 - - + +
620A ASP* 5.2 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 568 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A LEU* 4.0 25.8 - - - -
498A PRO* 4.3 7.0 - - - -
499A LEU* 4.2 17.5 - - - -
564A MET 3.0 17.0 + - - +
565A VAL 3.4 11.9 - - - +
566A LEU 3.4 0.2 - - - -
567A ARG* 1.3 84.7 - - - +
569A PRO* 1.4 66.9 - - - +
570A GLU* 2.9 31.5 + - - +
571A LEU* 3.0 23.4 + - + +
572A VAL 4.6 0.3 + - - -
----------------------------------------------------------
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