Contacts of the helix formed by residues 71 - 80 (chain J) in PDB entry 6NMY
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 ALA 71 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65J VAL* 3.8 24.5 - - + +
68J LEU* 3.4 33.3 + - + +
69J GLN 4.4 0.2 - - - +
70J ASN* 1.3 77.4 - - - +
72J SER* 1.3 60.2 + - - +
73J ALA 3.3 2.9 - - - -
74J ILE* 3.2 13.7 + - + -
75J GLU* 2.8 33.4 + - - +
104J TRP* 5.8 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 72 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A GLN* 5.6 3.3 + - - -
102A SER* 4.9 9.2 - - - -
70J ASN* 3.6 4.8 - - - -
71J ALA* 1.3 78.7 + - - +
73J ALA* 1.3 58.0 + - - +
75J GLU* 3.7 10.0 + - - +
76J SER* 2.9 31.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 73 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A SER* 4.5 12.9 + - - +
104A VAL* 3.9 16.4 - - + -
26J HIS* 3.5 43.3 - - + +
70J ASN 5.4 0.2 + - - -
71J ALA 3.3 0.4 - - - -
72J SER* 1.3 79.0 - - - +
74J ILE* 1.3 65.4 + - + +
76J SER* 3.3 3.7 + - - -
77J ILE* 3.0 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 74 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23J ILE* 3.8 31.9 - - + +
26J HIS* 3.6 42.4 - - + +
27J LEU* 4.8 6.1 - - + -
65J VAL* 4.3 4.3 - - + -
70J ASN 4.3 6.5 - - - +
71J ALA* 3.2 21.8 + - + +
73J ALA* 1.3 75.5 - - + +
75J GLU* 1.3 58.3 + - - +
77J ILE* 3.4 0.6 + - - -
78J LEU* 2.9 44.5 + - + +
104J TRP* 4.7 11.7 - - + -
107J PHE* 4.0 21.1 - - + -
111J LEU* 4.0 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 75 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62J ASN* 4.5 1.5 - - - +
65J VAL* 3.9 40.8 - - + +
66J LYS* 4.7 18.0 - - - +
71J ALA* 2.8 19.9 + - - +
72J SER* 3.7 9.3 - - - +
74J ILE* 1.3 76.7 - - - +
76J SER* 1.3 63.4 + - - +
78J LEU* 3.3 3.0 + - - +
79J LYS* 3.0 49.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 76 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A VAL* 4.3 9.9 - - - -
106A THR* 3.4 22.7 - - - +
107A ASP* 3.7 13.5 + - - -
72J SER 2.9 19.6 + - - -
73J ALA* 3.7 4.7 - - - -
75J GLU* 1.3 77.9 - - - +
77J ILE* 1.3 63.0 + - - +
79J LYS* 3.5 7.5 + - - +
80J ASN* 3.1 26.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 77 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A VAL* 3.6 34.5 - - + -
105A VAL 5.6 0.2 - - - +
106A THR* 4.6 7.9 - - - +
19J MET* 3.8 37.7 - - + +
22J GLU* 3.7 27.4 - - + +
23J ILE* 3.8 29.4 - - + +
26J HIS* 5.3 1.6 - - + -
73J ALA 3.0 16.5 + - - +
74J ILE 4.0 2.7 - - - +
76J SER* 1.3 75.9 - - - +
78J LEU* 1.3 65.2 + - - +
80J ASN* 3.1 14.0 + - - -
81J LEU* 3.3 16.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 78 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23J ILE* 3.7 19.1 - - + -
58J LEU* 4.0 16.8 - - + +
61J PHE* 4.0 27.8 - - + -
62J ASN* 3.5 24.4 + - - +
65J VAL* 4.6 7.0 - - + -
74J ILE* 2.9 36.2 + - + +
75J GLU* 3.8 3.1 - - - +
77J ILE* 1.3 76.2 - - - +
79J LYS* 1.3 62.7 + - - +
80J ASN 3.3 0.2 + - - -
81J LEU* 3.4 34.1 + - + +
82J LEU 4.9 0.2 + - - -
107J PHE* 4.1 7.4 - - + -
111J LEU* 4.1 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 79 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62J ASN* 4.0 16.8 - - + +
75J GLU* 3.0 41.1 + - + +
76J SER* 3.6 9.9 - - - +
77J ILE 3.1 0.4 - - - -
78J LEU* 1.3 79.1 - - - +
80J ASN* 1.3 64.3 + - - +
81J LEU 3.7 0.7 + - - -
82J LEU* 4.8 5.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 80 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A THR* 3.3 34.9 - - - +
19J MET* 3.3 17.9 - - + +
76J SER 3.1 17.8 + - - -
77J ILE 3.1 5.9 + - - +
79J LYS* 1.3 84.4 - - - +
81J LEU* 1.3 60.4 + - - +
82J LEU 3.3 3.1 + - - +
83J PRO* 3.7 12.4 - - - +
84J CYS* 4.9 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