Contacts of the helix formed by residues 62 - 73 (chain A) in PDB entry 4KPE
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 SER 62 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ARG 3.3 3.5 + - - -
61A LYS* 1.3 70.5 - - - +
63A ALA* 1.3 59.6 + - - +
64A LYS 3.2 0.2 + - - -
65A SER* 3.2 9.2 + - - -
66A VAL* 2.9 30.8 + - - +
82A TYR* 3.6 21.6 - - - -
85A MET* 4.8 4.9 - - - -
101A MET* 4.1 8.3 - - - +
116A MET* 3.7 5.6 - - - -
119A THR* 2.6 44.1 + - - -
120A GLU* 3.7 8.0 + - - -
121A ALA* 4.1 5.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LYS* 3.0 4.1 + - + -
62A SER* 1.3 78.6 - - - +
64A LYS* 1.3 61.7 + - - +
66A VAL* 4.0 0.7 - - - +
67A GLY* 3.0 18.2 + - - -
116A MET* 3.4 40.4 + - + +
117A ARG* 4.9 0.2 - - - -
63B ALA 4.9 0.2 - - - +
67B GLY* 3.7 13.3 - - - -
70B MET* 3.7 35.4 - - + -
78B ASP* 5.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ARG* 3.8 40.2 - - + +
61A LYS* 2.8 15.0 + - + +
63A ALA* 1.3 78.1 - - - +
65A SER* 1.3 64.8 + - - +
67A GLY* 3.5 0.9 + - - -
68A ASN* 3.1 35.9 + - - +
64B LYS 5.7 0.2 - - - +
67B GLY 3.6 19.9 + - - +
68B ASN* 3.4 26.0 + - - +
71B GLY* 4.0 17.8 + - - -
72B ASN* 3.1 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A SER* 4.7 0.4 + - - -
48A MET* 4.5 14.5 - - - +
51A ASP* 5.6 1.6 - - - -
53A ASN* 3.1 28.6 + - - -
60A ARG* 4.2 5.7 + - - +
61A LYS 3.4 6.5 + - - -
62A SER* 3.2 10.9 + - - -
64A LYS* 1.3 75.3 - - - +
66A VAL* 1.3 65.8 + - - +
68A ASN* 3.0 10.0 + - - +
69A ILE* 3.0 29.1 + - - +
85A MET* 4.4 15.9 - - - -
121A ALA* 5.4 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A SER 2.9 23.5 + - - +
63A ALA 4.0 3.4 - - - +
65A SER* 1.3 74.4 - - - +
67A GLY* 1.3 57.6 + - - +
69A ILE* 3.3 10.1 + - - +
70A MET* 3.0 43.2 + - + +
78A ASP* 3.5 26.0 - - + +
81A ILE* 4.3 9.0 - - + +
82A TYR* 4.0 37.2 - - + +
85A MET* 4.2 10.3 - - - -
116A MET* 3.9 13.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ALA 3.0 17.6 + - - -
64A LYS 3.9 0.9 - - - -
66A VAL* 1.3 77.3 - - - +
68A ASN* 1.3 60.8 + - - +
70A MET* 3.5 7.3 + - - +
71A GLY 3.1 16.8 + - - -
63B ALA* 3.7 25.4 - - - -
64B LYS* 3.4 21.6 + - - +
67B GLY* 5.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A SER* 4.1 5.6 - - - +
51A ASP* 3.2 31.9 + - - +
60A ARG* 5.9 2.0 - - - +
64A LYS* 3.1 27.7 + - - +
65A SER* 3.0 9.6 + - - +
67A GLY* 1.3 74.8 - - - +
69A ILE* 1.3 65.7 + - - +
71A GLY 3.3 0.2 + - - -
72A ASN* 3.0 39.9 + - - +
64B LYS* 3.6 26.3 - - - +
68B ASN* 3.7 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A VAL* 6.1 0.2 - - + -
43A ARG* 4.4 13.9 - - + -
44A ILE* 3.5 41.7 - - + +
47A SER* 3.7 24.9 - - - +
48A MET* 4.9 5.2 - - + +
65A SER* 3.0 20.6 + - - +
66A VAL* 3.4 7.4 - - - +
68A ASN* 1.3 75.3 - - - +
70A MET* 1.3 59.1 + - - +
73A PHE* 3.1 13.5 + - + -
74A HIS* 2.9 43.2 + - + -
81A ILE* 3.7 24.9 - - + -
85A MET* 5.2 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A VAL* 3.0 23.0 + - + +
67A GLY* 3.7 5.8 - - - +
69A ILE* 1.3 78.5 - - - +
71A GLY* 1.3 58.5 + - - +
74A HIS 3.4 20.5 - - - +
75A PRO* 4.3 3.8 - - + +
76A HIS 3.6 21.5 - - - +
78A ASP* 2.7 48.9 - - + +
81A ILE* 3.8 6.3 - - + -
145A PHE* 4.2 7.8 - - - -
61B LYS* 4.4 17.7 - - + +
63B ALA* 3.7 26.0 - - + -
117B ARG* 4.2 17.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLY 3.1 15.0 + - - -
68A ASN 3.3 0.9 + - - -
69A ILE 3.2 0.2 - - - -
70A MET* 1.3 77.8 - - - +
72A ASN* 1.3 68.7 + - - +
145A PHE* 3.6 15.1 - - - -
146A ASP* 4.6 6.8 - - - +
61B LYS* 4.2 17.6 - - - +
64B LYS* 4.2 14.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A SER* 4.9 0.8 + - - -
50A LYS* 5.9 3.0 - - - +
51A ASP* 5.5 2.8 + - - -
68A ASN* 3.0 30.1 + - - +
71A GLY* 1.3 84.2 - - - +
73A PHE* 1.3 85.3 + - + +
144A ASN* 2.7 34.3 + - - +
145A PHE* 3.6 4.4 - - - -
149A GLU* 4.0 14.6 + - - +
64B LYS* 3.0 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ARG* 3.5 42.6 + - + -
46A TYR* 3.5 30.7 - + - -
47A SER* 3.7 40.2 - - - -
50A LYS* 4.5 6.7 - - + -
69A ILE* 3.1 8.9 + - - +
72A ASN* 1.3 105.2 - - + +
74A HIS* 1.3 61.5 - - - +
75A PRO* 3.4 3.8 - - - +
144A ASN* 4.5 4.7 - - + -
145A PHE* 3.3 20.5 + - - +
149A GLU* 3.5 30.1 - - + -
150A LYS 4.3 2.9 - - - -
151A GLU* 3.9 25.2 - - + +
----------------------------------------------------------
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