Contacts of the helix formed by residues 600 - 615 (chain A) in PDB entry 1N1M
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 THR 600 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594A ILE* 4.6 0.3 - - - +
597A ARG* 2.7 31.6 + - + +
599A GLY* 1.3 84.4 - - - +
601A PHE* 1.3 85.3 + - - -
602A GLU* 2.9 5.2 + - - -
603A VAL* 2.7 20.4 - - - +
604A GLU* 2.8 33.7 + - - +
682A HIS* 3.5 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 601 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581A ARG* 3.2 55.0 - - + +
593A ALA* 3.4 31.9 - - + -
594A ILE* 4.0 4.9 - - + -
597A ARG* 5.3 9.2 - - + -
600A THR* 1.3 94.7 + - - +
602A GLU* 1.3 55.7 + - - +
604A GLU* 4.2 17.0 - - - -
605A ASP* 2.7 40.0 + - - -
782A NAG 4.4 5.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 602 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A ALA* 3.8 28.3 - - + +
580A GLY* 5.5 1.2 - - - -
581A ARG 3.6 22.6 + - - +
594A ILE* 3.9 17.0 - - + +
598A LEU* 3.8 2.6 - - - +
599A GLY* 2.8 23.4 + - - -
600A THR 2.9 20.6 + - - -
601A PHE* 1.3 75.0 + - - +
603A VAL* 1.3 63.2 + - - +
605A ASP* 4.1 4.3 - - - +
606A GLN* 3.3 27.5 + - - +
631A TYR* 2.6 27.8 + - - -
634A TYR* 4.5 0.9 - - - -
635A VAL* 4.0 18.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 603 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599A GLY* 3.1 36.3 - - - +
600A THR* 2.7 18.6 - - - +
602A GLU* 1.3 76.1 - - + +
604A GLU* 1.3 66.6 + - + +
606A GLN* 3.2 6.6 - - - +
607A ILE* 3.1 27.5 + - + +
635A VAL* 4.2 16.6 - - + -
638A MET* 4.2 22.4 - - + +
639A VAL* 3.8 23.6 - - + +
642A SER* 5.4 1.6 - - - -
691A ARG* 5.6 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 604 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581A ARG* 4.9 2.8 + - - +
600A THR* 2.8 38.6 + - - +
601A PHE* 3.7 20.3 + - - +
603A VAL* 1.3 78.1 - - + +
605A ASP* 1.3 63.5 + - - +
607A ILE* 3.0 17.1 + - + +
608A GLU* 2.9 27.8 + - - +
782A NAG 5.2 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 605 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A LEU* 4.5 8.3 - - + +
524A PHE* 4.8 1.0 - - - -
578A PHE* 3.6 20.6 - - + -
580A GLY* 3.7 6.6 - - - -
581A ARG* 2.6 66.9 + - - +
601A PHE 2.7 20.1 + - - +
602A GLU 4.1 3.4 - - - +
604A GLU* 1.3 73.7 - - - +
606A GLN* 1.3 56.0 + - - +
608A GLU* 3.7 8.5 - - - +
609A ALA* 2.9 30.3 + - - +
782A NAG 3.5 8.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 606 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A LEU* 3.5 46.7 - - + +
546A VAL* 3.7 34.0 - - + +
548A ALA* 4.1 6.8 - - - +
578A PHE* 3.3 38.2 + - - +
580A GLY 5.1 1.7 + - - -
602A GLU 3.3 14.5 + - - +
603A VAL* 3.2 16.8 + - - +
605A ASP* 1.3 80.0 - - - +
607A ILE* 1.3 59.9 + - - +
609A ALA* 3.7 3.5 - - - +
610A ALA* 3.2 23.6 + - - +
626A ILE* 4.7 4.7 - - + -
635A VAL* 4.2 6.3 - - + -
639A VAL* 4.5 4.9 - - + -
647A PHE* 5.0 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 607 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A VAL* 3.1 21.7 + - + +
604A GLU* 3.0 18.0 + - + +
606A GLN* 1.3 75.2 - - - +
608A GLU* 1.3 57.1 + - - +
610A ALA* 3.3 3.1 + - - +
611A ARG* 2.8 67.5 + - - +
639A VAL* 4.0 18.6 - - + -
642A SER* 3.7 30.5 - - - +
644A SER* 3.8 12.8 - - - +
646A VAL* 4.3 5.4 - - + +
647A PHE* 4.4 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 608 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A ILE* 5.7 0.4 - - - -
519A LEU* 4.0 18.6 - - + +
604A GLU 2.9 15.6 + - - +
605A ASP* 3.7 10.1 - - - +
607A ILE* 1.3 76.6 - - - +
609A ALA* 1.3 58.0 + - - +
611A ARG* 3.2 35.8 + - - +
612A GLN* 2.8 63.0 + - - +
782A NAG 6.0 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 609 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A ILE* 4.7 8.7 - - + +
519A LEU* 6.0 0.2 - - - +
544A LEU* 5.8 0.4 - - + -
578A PHE* 3.5 39.3 - - + -
605A ASP 2.9 17.7 + - - +
606A GLN* 3.7 5.4 - - - +
607A ILE 3.2 0.2 - - - -
608A GLU* 1.3 74.2 - - - +
610A ALA* 1.3 60.9 + - - +
612A GLN* 2.8 23.9 + - - +
613A PHE* 2.8 28.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 610 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A LEU* 5.5 1.3 - - + -
544A LEU* 4.2 7.6 - - + -
606A GLN 3.2 8.8 + - - +
607A ILE 3.8 2.5 - - - +
609A ALA* 1.3 78.9 - - - +
611A ARG* 1.3 62.9 + - - +
613A PHE* 3.2 16.1 + - + +
614A SER* 3.0 24.3 + - - -
624A ILE* 4.3 12.0 - - + +
646A VAL* 4.3 6.5 - - + -
647A PHE* 3.3 39.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 611 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A ILE* 2.8 49.1 + - - +
608A GLU* 3.2 32.9 + - - +
610A ALA* 1.3 77.8 - - - +
612A GLN* 1.3 58.5 + - + +
614A SER* 2.7 23.5 + - - +
615A LYS* 3.5 17.7 + - + +
644A SER* 3.8 14.3 + - - +
646A VAL* 3.7 26.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 612 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A ILE* 3.4 39.7 - - + +
518A ILE 4.4 5.1 + - - +
519A LEU* 3.4 13.5 - - - +
608A GLU* 2.8 41.1 + - - +
609A ALA* 2.8 8.7 + - - +
611A ARG* 1.3 75.5 - - + +
613A PHE* 1.3 69.3 + - + +
615A LYS* 3.5 15.0 + - - +
616A MET* 3.4 15.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 613 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A ILE* 5.3 5.6 - - + -
526A TYR* 3.8 51.1 - + + -
528A MET* 4.6 9.2 - - - -
542A LEU* 3.9 30.3 - - + -
544A LEU* 4.3 12.6 - - + -
576A ALA* 4.3 17.0 - - + -
577A SER 4.8 0.2 - - - -
578A PHE* 4.5 4.7 - + + -
609A ALA* 2.8 41.5 + - + -
610A ALA* 3.2 17.2 + - + +
612A GLN* 1.3 79.1 - - + +
614A SER* 1.3 58.5 + - - +
616A MET* 2.8 44.7 - - - +
619A VAL* 3.2 11.8 - - + +
624A ILE* 5.9 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 614 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A LYS* 5.3 1.0 + - - -
610A ALA 3.0 7.9 + - - -
611A ARG* 2.7 26.7 + - - +
613A PHE* 1.3 72.4 - - - +
615A LYS* 1.3 62.9 + - - +
616A MET 2.5 18.2 + - - -
617A GLY 3.7 4.2 + - - -
619A VAL* 3.5 27.9 - - - +
621A ASN* 3.9 20.0 - - - +
624A ILE* 3.4 25.8 - - - -
646A VAL* 5.5 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 615 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A ARG* 3.5 22.0 + - + +
612A GLN* 3.5 12.1 + - - +
613A PHE 3.3 0.8 - - - -
614A SER* 1.3 82.6 + - - +
616A MET* 1.3 58.5 + - - +
617A GLY 3.8 0.9 - - - -
----------------------------------------------------------
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