Contacts of the helix formed by residues 598 - 606 (chain A) in PDB entry 4MXP
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 LYS 598 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556A LYS* 3.4 37.8 - - - +
575A PHE* 4.4 6.3 - - + -
594A GLU* 3.4 32.0 + - - +
595A LEU* 3.0 38.1 + - + +
596A LYS 4.1 0.2 - - - +
597A SER* 1.3 82.5 - - - +
599A ASP* 1.3 63.8 + - - +
600A GLU* 3.4 14.3 + - + +
601A TYR* 2.9 17.5 + - - +
602A ARG* 3.2 13.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 599 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552A PHE* 3.7 13.4 - - + +
553A LYS* 3.3 9.9 + - - +
554A ASN* 2.8 42.6 + - - +
555A VAL* 3.5 21.1 - - + +
597A SER 3.9 0.2 + - - -
598A LYS* 1.3 73.1 - - - +
600A GLU* 1.3 66.2 + - - +
602A ARG* 2.8 41.3 + - - +
603A ILE* 3.0 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 600 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554A ASN 4.4 3.5 - - - +
555A VAL* 3.6 11.0 - - + -
556A LYS* 2.9 51.4 + - - +
559A TYR* 3.4 31.6 - - + +
571A ILE* 3.8 20.0 - - + +
575A PHE* 3.8 20.2 - - + -
598A LYS* 3.4 16.2 - - + +
599A ASP* 1.3 78.6 + - - +
601A TYR* 1.3 61.2 + - - +
603A ILE* 3.3 9.6 + - - +
604A LEU* 3.2 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 601 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575A PHE* 3.8 22.2 - + + -
595A LEU 3.4 16.6 - - - +
596A LYS* 3.7 51.8 + - + -
598A LYS 2.9 11.3 + - - +
600A GLU* 1.3 80.1 - - - +
602A ARG* 1.3 66.7 + - + +
604A LEU* 3.0 10.6 + - + +
605A ALA* 3.0 29.7 + - + +
622A VAL* 3.6 35.4 - - + +
625A PHE* 3.8 25.6 - + - -
626A GLU* 4.6 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 602 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552A PHE* 3.6 21.2 - - + -
596A LYS 5.2 3.3 + - - +
597A SER* 3.0 33.2 + - - +
598A LYS 3.2 2.8 + - - +
599A ASP* 2.8 49.6 + - - +
601A TYR* 1.3 83.6 - - + +
603A ILE* 1.3 56.3 + - - +
605A ALA* 3.3 6.0 + - - +
606A LYS* 3.0 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 603 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A ALA* 4.3 12.5 - - + +
548A SER 3.9 15.0 - - - +
549A THR* 4.1 13.2 - - + -
552A PHE* 3.6 26.0 - - + -
555A VAL* 3.8 29.2 - - + -
567A LEU* 3.9 17.5 - - + -
568A LYS* 3.3 18.6 + - + -
571A ILE* 3.9 20.9 - - + -
599A ASP 3.0 13.7 + - - +
600A GLU* 3.4 11.9 - - - +
602A ARG* 1.3 73.8 - - - +
604A LEU* 1.3 65.5 + - - +
606A LYS* 3.3 16.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 604 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A LYS* 2.9 50.0 + - + +
571A ILE* 3.7 19.7 - - + -
572A LEU* 3.9 24.5 - - + -
575A PHE* 3.9 25.8 - - + -
600A GLU 3.2 13.1 + - - +
601A TYR* 3.0 15.9 + - + +
603A ILE* 1.3 77.6 - - - +
605A ALA* 1.3 55.2 + - - +
619A THR* 2.7 23.6 + - - -
621A SER* 3.1 25.4 + - - +
622A VAL* 4.0 7.4 - - + -
625A PHE* 4.6 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 605 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A TYR* 3.0 26.9 + - + +
602A ARG* 3.9 6.7 - - - +
603A ILE 3.2 0.2 - - - -
604A LEU* 1.3 76.3 - - - +
606A LYS* 1.3 60.8 + - - +
607A GLY 3.5 2.9 + - - -
612A THR* 5.3 0.3 - - - +
617A LEU 4.8 4.9 - - - +
619A THR* 3.5 10.8 + - - +
622A VAL* 3.5 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 606 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A TYR* 5.8 3.1 - - - -
546A THR 5.8 0.8 + - - -
547A ALA* 5.7 6.2 - - - +
548A SER* 4.7 13.2 + - - +
551A ASN* 3.6 23.6 + - - +
552A PHE* 3.6 32.0 - - + -
568A LYS* 2.9 25.6 + - - -
602A ARG 3.0 16.6 + - - +
603A ILE* 3.3 7.7 + - - +
605A ALA* 1.3 76.5 - - - +
607A GLY* 1.3 73.0 + - - +
608A GLN* 4.3 1.0 - - - +
613A GLN* 4.1 13.5 - - + +
619A THR* 3.9 1.1 - - - -
----------------------------------------------------------
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