Contacts of the helix formed by residues 63 - 75 (chain B) in PDB entry 1KYO
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 63 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ASN* 3.2 20.9 - - - -
59B THR 4.5 0.6 + - - -
62B ARG* 1.3 78.9 - - - +
64B ALA* 1.3 65.1 + - - +
65B LEU* 4.0 4.7 + - - -
66B LYS* 3.4 10.5 + - - +
67B LEU* 3.2 17.8 + - - +
116R GLU* 2.7 39.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A LEU* 3.9 19.7 - - + -
56B PHE 3.8 11.1 - - - +
57B GLN* 3.7 33.6 + - - +
58B ASN* 2.6 17.0 + - - +
62B ARG 3.7 0.4 + - - -
63B SER* 1.3 72.3 - - - +
65B LEU* 1.3 63.0 + - - +
67B LEU* 3.4 7.4 + - - +
68B VAL* 3.1 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A LEU* 3.4 35.7 - - + +
63B SER* 3.2 6.8 - - - +
64B ALA* 1.3 79.3 - - - +
66B LYS* 1.3 57.8 + - - +
68B VAL* 3.2 4.3 + - - +
69B ARG* 2.9 63.9 + - - +
113R ALA 5.1 2.0 - - - +
116R GLU* 4.5 7.2 - - - +
117R LYS* 3.8 44.2 - - + +
120R LEU* 3.9 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ARG* 4.5 19.7 - - + +
63B SER* 3.4 19.7 + - - +
65B LEU* 1.3 75.9 - - - +
67B LEU* 1.3 65.0 + - - +
69B ARG* 4.4 0.9 - - - -
70B GLU* 2.9 49.4 + - + +
116R GLU* 3.5 18.3 + - - +
120R LEU* 3.7 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B PHE* 4.1 37.9 - - + +
57B GLN 5.1 4.0 - - - +
59B THR* 5.7 4.3 - - + -
62B ARG* 3.7 37.5 - - + +
63B SER 3.2 12.8 + - - +
64B ALA 3.6 9.9 - - - +
65B LEU 3.2 0.4 - - - -
66B LYS* 1.3 75.8 - - - +
68B VAL* 1.3 60.0 + - + +
71B SER* 2.9 32.4 + - - -
78B PHE* 3.7 27.4 - - + -
100B TYR* 3.6 18.1 + - + +
104B ALA* 4.5 3.1 - - + +
108B VAL* 4.8 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ALA* 4.3 22.4 - - + +
296A LEU* 3.9 35.4 - - + +
297A GLN* 4.5 0.9 - - + -
56B PHE 6.1 0.9 - - - +
64B ALA 3.1 16.2 - - - +
65B LEU 3.2 5.3 + - - +
67B LEU* 1.3 76.3 - - + +
69B ARG* 1.3 68.3 + - - +
71B SER* 2.8 10.4 + - - +
72B GLU* 2.8 47.5 + - + +
78B PHE* 5.7 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A LEU 2.3 33.3 + - - -
297A GLN 3.2 13.1 + - - -
298A GLY* 3.4 24.8 - - - +
299A ILE 4.9 0.8 + - - +
65B LEU* 2.9 38.4 + - + +
66B LYS* 4.0 5.6 - - - +
68B VAL* 1.3 74.0 - - - +
70B GLU* 1.3 62.9 + - - +
72B GLU* 3.3 9.1 + - - +
73B LEU* 3.0 34.9 + - + +
117R LYS* 4.5 12.1 + - - +
120R LEU* 3.6 42.9 + - + -
121R ASP* 2.7 26.3 + - - +
123R ILE* 5.7 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ARG* 3.3 23.0 + - - -
66B LYS* 2.9 36.5 + - + +
69B ARG* 1.3 73.7 - - - +
71B SER* 1.3 64.9 + - - +
73B LEU* 3.0 20.0 + - - +
74B LEU* 3.3 19.0 + - + +
100B TYR* 3.0 34.4 + - + +
120R LEU* 6.0 0.6 - - - +
123R ILE* 6.3 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LEU 2.9 18.7 + - - -
68B VAL* 2.8 21.7 + - - +
70B GLU* 1.3 75.9 - - - +
72B GLU* 1.3 58.0 + - - +
74B LEU* 3.1 5.4 + - - +
75B GLY 2.9 24.3 + - - -
76B GLY 3.2 24.5 + - - -
77B THR* 5.0 0.3 - - - -
78B PHE* 3.6 27.1 - - - -
100B TYR* 3.8 16.7 + - - -
101B TYR* 4.0 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A GLN* 3.6 24.4 - - - +
298A GLY* 3.2 18.5 + - - -
364A ARG* 2.8 46.8 + - + +
367A SER* 3.4 7.6 - - - -
368A LEU* 3.4 32.6 - - + +
68B VAL* 2.8 29.8 + - + +
69B ARG* 3.4 13.6 - - - +
70B GLU 3.1 0.2 + - - -
71B SER* 1.3 78.6 - - - +
73B LEU* 1.3 63.4 + - + +
74B LEU 3.2 0.7 + - - -
75B GLY 3.2 8.1 + - - -
76B GLY 4.5 2.5 - - - +
77B THR* 6.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A THR* 4.5 9.2 - - - +
363A GLU* 4.6 3.6 - - + -
364A ARG* 4.1 33.2 - - + +
367A SER* 2.8 18.8 + - - -
69B ARG* 3.0 32.1 + - + +
70B GLU* 3.0 11.2 + - - +
72B GLU* 1.3 81.7 - - + +
74B LEU* 1.3 61.5 + - + +
123R ILE* 4.1 26.2 - - + -
125R VAL* 4.2 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A SER* 3.9 5.2 + - - -
370A LYS* 5.9 0.2 - - - -
70B GLU* 3.7 13.2 - - + +
71B SER* 3.1 7.3 + - - +
72B GLU 3.1 0.4 - - - -
73B LEU* 1.3 84.1 - - + +
75B GLY* 1.3 59.2 + - - +
94B LEU* 3.8 12.0 - - - +
97B ASP* 3.6 30.1 - - + +
100B TYR* 3.4 54.3 - - + -
101B TYR* 3.5 14.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A SER* 3.6 23.6 - - - -
368A LEU* 4.4 2.7 - - - -
371A LEU* 3.9 9.6 - - - +
71B SER 2.9 7.2 + - - -
72B GLU 3.2 9.5 + - - -
74B LEU* 1.3 79.6 - - - +
76B GLY* 1.3 55.7 + - - -
93B PHE* 3.7 2.1 - - - -
94B LEU* 3.5 32.3 + - - +
101B TYR* 3.8 3.2 + - - -
----------------------------------------------------------
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