Contacts of the helix formed by residues 612 - 623 (chain A) in PDB entry 3MXN
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 ASN 612 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609A GLN* 4.1 11.3 - - - +
610A ASP 4.2 3.5 + - - +
611A VAL* 1.3 75.1 - - - +
613A MET* 1.3 64.0 + - - +
614A GLU* 3.0 27.2 + - - +
615A HIS* 2.9 51.0 + - - +
616A LEU 3.2 8.5 + - - -
130B ILE* 3.6 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 613 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A BEN 3.4 41.0 + - + +
612A ASN* 1.3 72.1 - - - +
614A GLU* 1.3 59.1 + - - +
616A LEU* 3.2 31.2 + - + +
617A GLU* 2.9 42.6 + - + +
130B ILE* 3.1 32.5 - - + +
133B SER* 5.5 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 614 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A BEN 3.7 44.5 + - + -
612A ASN* 3.0 15.8 + - - +
613A MET* 1.3 78.0 - - - +
615A HIS* 1.3 62.6 + - + +
617A GLU* 3.2 1.9 + - - +
618A ASN* 2.8 50.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 615 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A PRO* 3.5 26.1 - - + +
491A PHE* 5.8 0.4 - - + -
509A LYS* 4.5 3.9 + - - -
591A LEU* 3.5 22.7 - - + +
609A GLN* 3.2 29.7 + - - -
610A ASP 3.6 11.0 - - - -
611A VAL* 3.4 7.8 - - + -
612A ASN* 2.9 48.6 + - - +
614A GLU* 1.3 80.5 + - + +
616A LEU* 1.3 61.7 + - - +
618A ASN* 3.3 14.9 + - - +
619A LEU* 2.9 20.6 + - - +
134B MET* 4.2 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 616 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A ASN 3.2 7.0 + - - +
613A MET* 3.4 39.0 - - + +
615A HIS* 1.3 77.9 - - - +
617A GLU* 1.3 58.4 + - - +
619A LEU* 3.2 4.0 + - + +
620A LYS* 2.9 36.4 + - + +
130B ILE* 4.5 3.4 - - + -
133B SER* 3.8 28.5 - - - +
134B MET* 3.1 33.3 - - + -
137B LEU* 3.3 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 617 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A BEN 4.1 22.9 - - + +
613A MET* 2.9 36.0 + - + +
614A GLU 3.2 4.2 + - - +
616A LEU* 1.3 72.9 - - - +
618A ASN* 1.3 60.7 + - - +
620A LYS* 3.4 36.1 + - - +
621A LYS* 2.9 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 618 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A PRO* 3.7 31.9 - - + +
490A PRO* 3.7 20.6 - - + +
614A GLU* 2.8 41.2 + - - +
615A HIS* 3.3 20.4 - - - +
617A GLU* 1.3 76.6 - - - +
619A LEU* 1.3 57.3 + - - +
621A LYS* 3.4 10.1 + - - +
622A ARG* 3.0 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 619 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A PRO* 3.8 10.7 - - + +
491A PHE* 4.4 8.1 - - + -
615A HIS 2.9 13.2 + - - +
616A LEU* 3.2 9.6 + - + +
618A ASN* 1.3 75.3 - - - +
620A LYS* 1.3 65.1 + - - +
622A ARG* 3.2 18.1 + - - +
623A LEU* 3.1 24.8 + - + +
134B MET* 4.3 15.9 - - + +
137B LEU* 3.6 30.7 - - + -
138B GLU* 3.8 26.0 - - + +
141B ASP* 3.6 37.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 620 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A LEU* 2.9 28.8 + - + +
617A GLU* 3.6 38.3 + - - +
619A LEU* 1.3 75.2 - - - +
621A LYS* 1.3 63.3 + - - +
623A LEU* 3.2 2.5 + - - -
624A ASN 3.0 4.7 + - - -
625A LYS* 2.8 54.0 + - + -
137B LEU* 3.6 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 621 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A GLU 2.9 17.9 + - - +
618A ASN* 3.6 9.0 - - - +
619A LEU 3.2 0.2 - - - -
620A LYS* 1.3 77.2 - - - +
622A ARG* 1.3 58.1 + - - +
624A ASN* 2.9 22.8 + - - +
625A LYS 4.9 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 622 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A SER* 3.1 44.0 + - - -
489A PRO 3.2 11.6 + - - +
490A PRO* 4.1 5.5 - - - +
491A PHE* 2.9 38.0 + - - -
492A VAL* 4.6 1.4 - - - +
493A TYR* 4.2 4.9 + - - -
618A ASN 3.0 13.6 + - - +
619A LEU* 3.2 17.7 + - - +
621A LYS* 1.3 77.6 - - - +
623A LEU* 1.3 58.6 + - - +
624A ASN* 3.2 1.1 + - - +
141B ASP* 2.8 41.7 + - - +
144B ARG* 3.3 21.3 + - - +
145B ASN* 5.6 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 623 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619A LEU* 3.1 16.3 + - + +
620A LYS 3.2 1.3 + - - +
622A ARG* 1.3 74.8 - - - +
624A ASN* 1.3 68.0 + - - +
625A LYS* 3.5 19.8 + - + +
137B LEU* 3.6 50.5 - - + +
140B GLU* 4.0 20.9 - - - +
141B ASP* 3.6 28.7 - - + +
144B ARG* 3.4 36.8 - - - +
----------------------------------------------------------
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