Contacts of the helix formed by residues 679 - 686 (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 ASN 679 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596A ARG* 3.1 41.7 - - - +
597A ARG* 3.2 26.3 - - - +
671A MET* 3.1 33.0 - - - +
673A LEU 3.1 9.4 + - - +
678A ASP* 1.3 83.0 + - - +
680A LEU* 1.3 65.8 + - - +
681A ASP* 3.3 3.9 - - - +
682A HIS* 3.4 11.2 - - - +
683A TYR* 3.0 15.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 680 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660A GLU* 4.3 3.4 - - - +
673A LEU 3.8 0.8 + - - -
674A PRO* 3.2 25.4 - - + +
675A THR 3.0 21.6 + - - +
676A PRO* 3.5 31.9 + - + +
678A ASP 3.8 0.6 - - - -
679A ASN* 1.3 76.0 - - - +
681A ASP* 1.3 64.9 + - - +
683A TYR* 2.9 19.7 + - + +
684A ARG* 3.0 55.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 681 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A ARG* 6.1 0.4 - - - +
676A PRO* 5.2 6.7 + - - +
679A ASN* 3.3 2.4 - - - +
680A LEU* 1.3 80.4 - - - +
682A HIS* 1.3 58.3 + - - +
684A ARG* 3.2 6.1 + - - +
685A ASN* 2.9 39.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 682 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596A ARG 3.7 0.9 - - - -
597A ARG* 3.1 50.6 - - - +
598A LEU 2.6 33.9 + - - -
599A GLY 5.0 0.2 - - - -
600A THR* 3.5 24.5 - - + -
671A MET* 3.3 28.5 - - + -
679A ASN* 3.4 12.4 + - - +
680A LEU 3.3 0.6 - - - -
681A ASP* 1.3 77.2 - - - +
683A TYR* 1.3 58.7 + - - +
685A ASN* 4.2 10.0 - - + +
686A SER* 2.7 47.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 683 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ALA* 3.9 13.7 - - + +
658A ARG* 5.4 0.2 - - - +
659A TRP* 3.8 31.8 + - + -
660A GLU* 3.5 30.1 - - + +
667A THR* 3.7 14.3 - - + +
668A GLU* 4.1 3.1 - - - +
671A MET* 3.4 44.9 - - + +
672A GLY 2.6 18.4 + - - -
673A LEU 3.5 2.2 - - - -
674A PRO* 3.5 38.7 - - + +
679A ASN 3.0 22.0 + - - -
680A LEU* 2.9 12.5 + - + +
682A HIS* 1.3 79.6 - - - +
684A ARG* 1.3 60.3 + - - +
686A SER* 3.4 9.7 + - - -
687A THR* 3.6 13.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 684 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658A ARG* 3.7 25.3 - - - +
660A GLU* 2.8 38.2 + - - -
674A PRO 5.5 0.2 + - - -
680A LEU* 3.0 40.6 + - + +
681A ASP* 3.7 8.7 - - - +
683A TYR* 1.3 76.8 - - - +
685A ASN* 1.3 65.4 + - - +
686A SER 3.5 0.3 + - - -
687A THR* 3.6 16.8 + - - +
690A SER* 4.9 5.9 - - - -
245B SER* 5.7 6.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 685 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681A ASP* 2.9 32.6 + - - +
682A HIS* 3.2 13.9 + - + +
684A ARG* 1.3 79.2 - - - +
686A SER* 1.3 58.5 + - - +
687A THR 3.6 1.2 + - - -
690A SER* 4.3 5.8 + - - -
691A ARG* 3.7 17.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 686 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A LEU 3.6 23.8 - - - -
599A GLY* 4.9 1.6 - - - -
634A TYR* 2.9 27.1 + - - -
638A MET* 3.7 10.8 - - - +
657A SER 4.4 0.2 - - - +
658A ARG* 5.3 0.4 - - - -
659A TRP* 3.7 18.5 - - - -
671A MET* 3.9 3.8 - - - +
682A HIS* 2.7 28.3 + - - -
683A TYR 3.4 6.8 + - - -
684A ARG 3.3 1.0 - - - -
685A ASN* 1.3 79.8 - - - +
687A THR* 1.3 62.3 + - - +
----------------------------------------------------------
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