Contacts of the helix formed by residues 57 - 68 (chain B) in PDB entry 1KLC
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 GLN 57 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TRP* 5.7 0.4 - - + -
101A LEU* 3.0 25.2 - - + +
102A SER* 2.3 57.9 + - - +
103A ASN* 3.1 12.7 - - + +
104A MET* 3.8 14.1 - - + +
56B THR* 1.3 69.4 - - - +
58B TYR* 1.3 58.1 + - - +
59B SER 2.9 10.1 + - - -
60B LYS* 3.1 47.0 + - + +
61B VAL* 3.4 4.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU* 4.2 2.5 - - + -
22A ILE* 5.2 0.2 - - + -
39A TYR* 4.7 3.4 - - - -
41A ALA* 4.2 18.2 - - + -
42A ASN 3.4 19.3 - - - -
43A PHE* 2.8 28.0 - - + +
44A CYS 4.5 0.7 + - - -
80A PRO* 3.3 36.6 - - + -
83A LEU* 3.7 14.4 - - + -
103A ASN 2.8 16.9 + - - +
104A MET* 4.8 2.7 - - - +
105A ILE 4.6 5.6 - - - +
106A VAL* 4.1 3.4 - - + -
56B THR* 3.2 2.8 + - - +
57B GLN* 1.3 76.1 - - - +
59B SER* 1.3 62.9 + - - +
60B LYS 3.3 0.4 - - - -
61B VAL* 4.0 7.2 - - + -
62B LEU* 2.6 66.3 + - + +
74B ALA 4.0 0.3 + - - -
75B ALA 4.4 0.3 + - - -
76B PRO* 5.3 1.6 - - + -
112B SER* 4.0 8.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B CYS* 5.9 0.2 - - - -
54B LEU* 2.9 30.4 - - - +
55B ASP 3.9 1.8 - - - -
56B THR* 2.7 37.7 + - - +
57B GLN 2.9 0.6 - - - -
58B TYR* 1.3 84.8 - - - +
60B LYS* 1.3 56.2 + - - +
62B LEU* 5.3 0.4 - - - -
63B ALA* 2.9 20.6 + - - +
76B PRO* 5.1 9.6 - - - +
111B CYS* 3.3 25.3 + - - -
112B SER* 4.1 3.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TRP* 4.4 16.2 - - + -
32A TRP* 6.3 1.1 - - - -
50B TYR* 4.8 2.8 - - + +
54B LEU* 3.0 40.0 - - + +
56B THR 3.9 0.8 + - - +
57B GLN* 3.1 38.9 + - + +
59B SER* 1.3 79.8 - - - +
61B VAL* 1.3 78.5 + - + +
63B ALA* 3.6 3.2 - - - +
64B LEU* 3.3 26.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE* 3.5 12.6 - - + -
28A LEU* 3.0 31.8 - - + +
30A TRP* 2.9 35.9 - - + -
39A TYR* 3.2 25.1 - - + +
104A MET* 3.2 21.8 - - + -
57B GLN 3.4 13.1 + - - +
58B TYR* 4.3 4.9 - - + +
60B LYS* 1.3 80.0 - - + +
62B LEU* 1.3 69.4 + - + +
64B LEU 2.9 11.6 + - - -
65B TYR 2.9 8.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU* 3.1 30.3 - - + -
22A ILE* 4.5 0.7 - - + -
58B TYR* 2.6 46.1 + - + +
61B VAL* 1.3 81.7 - - - +
63B ALA* 1.3 65.1 + - - +
65B TYR* 2.6 30.0 + - + -
66B ASN* 3.0 11.8 + - - +
74B ALA 2.7 22.0 - - - +
75B ALA* 3.0 32.5 - - - +
76B PRO* 3.0 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B CYS 4.0 9.6 - - - +
49B PRO 3.0 31.2 - - - +
50B TYR* 3.7 8.5 - - - -
59B SER 2.9 24.5 + - - +
60B LYS 3.6 7.2 - - - +
61B VAL 3.2 0.2 - - - -
62B LEU* 1.3 79.0 - - - +
64B LEU* 1.3 57.3 + - - +
66B ASN* 4.0 1.6 + - - +
67B GLN* 3.2 30.5 + - - +
76B PRO* 4.6 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LEU* 3.3 13.0 - - + -
30A TRP* 3.6 28.3 - - + +
50B TYR* 2.8 53.4 - - + -
60B LYS* 3.3 18.4 - - + +
61B VAL 2.9 2.3 + - - +
62B LEU 2.7 1.2 + - - -
63B ALA* 1.3 73.9 - - - +
65B TYR* 1.3 62.6 + - - +
66B ASN 3.0 2.7 - - - -
67B GLN* 4.0 0.4 - - - -
68B HIS* 2.7 59.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU* 3.1 30.5 - - + +
21A TYR 4.0 5.0 + - - -
22A ILE* 3.5 22.9 - - + -
27A ASP* 2.7 51.6 + - + -
28A LEU* 2.9 19.2 - - + +
61B VAL 2.9 0.2 + - - -
62B LEU* 2.6 42.0 + - + +
64B LEU* 1.3 73.1 - - - +
66B ASN* 1.3 62.1 + - - +
69B ASN* 3.4 28.6 + - - +
72B ALA* 4.7 11.4 - - + +
74B ALA* 4.0 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LEU 3.0 7.4 + - - +
63B ALA 4.4 2.2 - - - +
64B LEU 3.0 0.2 - - - -
65B TYR* 1.3 78.6 - - - +
67B GLN* 1.3 61.7 + - + +
68B HIS 2.7 11.2 + - - -
69B ASN 2.8 25.2 + - - +
71B GLY 5.8 0.4 - - - +
72B ALA* 2.3 34.9 + - - +
73B SER* 4.9 0.2 - - - +
74B ALA* 3.1 6.5 + - - +
75B ALA* 2.8 48.6 + - + +
76B PRO* 5.2 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ASN* 5.8 4.0 - - - +
48B CYS 5.3 1.3 - - - +
49B PRO* 4.7 16.4 - - + +
50B TYR* 2.6 45.0 + - + +
63B ALA 3.2 19.6 + - - +
64B LEU* 3.3 2.8 + - - -
66B ASN* 1.3 80.4 - - + +
68B HIS* 1.3 60.1 + - - +
69B ASN 5.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LYS 5.6 0.2 - - - +
27A ASP 2.9 26.6 + - - +
28A LEU 3.4 22.0 + - - -
29A GLY* 4.9 3.0 - - - -
50B TYR* 5.2 2.7 - - - -
64B LEU* 2.7 55.5 + - + +
66B ASN 2.7 0.6 + - - -
67B GLN* 1.3 83.5 - - - +
69B ASN* 1.3 62.7 + - - +
70B PRO* 3.1 12.2 - - - +
----------------------------------------------------------
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