Contacts of the helix formed by residues 38 - 51 (chain B) in PDB entry 3KSA
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 LYS 38 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ARG 3.7 9.4 - - - +
29B ALA* 3.1 35.4 - - - +
31B PRO* 4.1 9.2 - - + -
36B GLY 4.4 0.2 + - - -
37B LEU* 1.3 74.8 - - - +
39B PRO* 1.3 74.3 - - + +
40B VAL* 4.6 6.7 - - + +
41B GLN* 2.5 48.9 + - - +
42B ARG* 3.0 10.9 + - - -
87B ARG* 6.1 3.0 - - - +
167B SER* 4.1 11.4 + - - +
168B THR 2.9 32.2 + - - -
169B GLY 4.2 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B GLN 4.1 9.9 - - - +
27B ASP* 2.9 42.0 - - + +
28B ARG 4.2 4.0 - - - +
30B LEU 4.4 3.8 - - - +
37B LEU 4.1 3.8 - - - +
38B LYS* 1.3 87.4 - - + -
40B VAL* 1.3 60.4 + - + +
42B ARG* 3.0 25.3 + - - +
43B ARG* 2.8 53.8 + - - +
74B HIS* 5.2 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ASP 5.6 1.1 - - - +
28B ARG* 5.0 15.7 - - + +
38B LYS* 3.2 4.5 + - + -
39B PRO* 1.3 75.4 - - + +
41B GLN* 1.3 65.2 + - + +
43B ARG* 3.2 2.2 + - + +
44B ILE* 2.8 33.8 + - + +
69B ILE* 6.1 0.4 - - + -
74B HIS* 3.7 39.7 - - + +
80B SER* 4.7 2.9 - - - +
81B ILE* 4.1 27.4 - - + +
84B ALA* 4.2 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B GLY 4.7 0.9 - - - +
37B LEU* 3.5 23.9 - - + +
38B LYS* 2.5 63.5 + - - +
40B VAL* 1.3 80.7 - - + +
42B ARG* 1.3 63.3 + - - +
44B ILE* 3.1 2.6 + - - +
45B LEU* 2.9 28.0 + - - +
84B ALA* 5.5 6.8 + - + +
87B ARG* 5.7 6.7 - - - +
88B MET* 3.4 36.3 - - + +
167B SER* 5.0 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ASP* 3.6 22.2 + - - +
35B ASP* 2.9 18.1 + - - +
37B LEU* 2.9 39.1 + - + +
38B LYS 3.0 4.1 + - - +
39B PRO* 3.0 31.5 + - - +
41B GLN* 1.3 78.2 - - - +
43B ARG* 1.3 59.1 + - + +
45B LEU* 3.2 4.6 + - - +
46B TYR* 2.8 33.1 + - + +
151B GLU* 5.8 2.7 + - - +
152B PRO* 4.0 11.7 + - + +
153B THR* 3.7 16.2 + - - +
154B VAL* 3.5 26.9 - - - +
155B LEU* 3.5 27.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B TYR* 5.5 3.4 + - - -
27B ASP* 4.5 15.0 + - - -
39B PRO* 2.8 32.0 + - - +
40B VAL* 3.8 4.5 - - - +
42B ARG* 1.3 69.8 - - + +
44B ILE* 1.3 66.1 + - - +
46B TYR* 4.6 4.9 - - - -
47B SER* 3.0 28.1 + - - -
69B ILE* 4.3 10.0 - - + +
73B PHE* 3.6 38.2 + - + -
74B HIS* 2.6 49.8 + - - +
75B PRO* 4.3 6.8 - - - +
76B HIS* 4.8 2.4 + - - -
151B GLU* 2.6 40.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B VAL* 2.8 32.5 + - + +
41B GLN 3.3 4.5 - - - +
43B ARG* 1.3 77.2 - - - +
45B LEU* 1.3 65.1 + - - +
47B SER* 3.7 0.3 - - - -
48B MET* 2.9 49.1 + - - +
69B ILE* 3.6 21.5 - - + -
81B ILE* 3.5 38.1 - - + +
84B ALA* 4.6 0.9 - - + -
85B MET* 3.6 23.3 - - + +
88B MET* 3.6 24.2 - - + -
99B VAL* 5.2 0.4 - - + -
123B LEU* 5.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 3.6 31.0 - - + -
41B GLN 2.9 20.6 + - - +
42B ARG 3.5 6.1 - - - +
44B ILE* 1.3 76.3 - - - +
46B TYR* 1.3 64.0 + - - +
49B ASN* 3.0 26.3 + - - +
88B MET* 4.6 10.1 - - + -
98B LEU* 3.8 25.4 - - + -
99B VAL* 5.9 0.7 - - + -
123B LEU* 3.5 22.5 - - + +
127B ALA* 4.0 30.3 - - + +
130B LEU* 4.7 4.0 - - + -
131B LEU* 4.4 13.5 - - + -
155B LEU* 4.3 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ARG* 2.8 21.5 + - + +
43B ARG* 4.1 3.8 - - - +
45B LEU* 1.3 72.4 - - - +
47B SER* 1.3 58.9 + - - +
49B ASN* 3.2 4.8 + - - +
50B LYS* 2.8 46.9 + - + +
73B PHE* 3.5 41.1 - + - -
131B LEU* 4.1 14.8 - - + +
134B ILE* 4.5 15.3 - - + -
141B PHE* 3.8 13.9 - + - -
149B GLU* 4.1 6.2 + - - -
150B LYS 3.2 14.8 + - - -
151B GLU* 4.9 1.3 - - + -
152B PRO* 3.2 44.0 - - + -
155B LEU* 5.1 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ARG 3.0 20.4 + - - -
44B ILE 3.7 1.6 - - - -
46B TYR* 1.3 78.7 - - - +
48B MET* 1.3 66.4 + - - +
50B LYS* 3.2 5.2 + - - +
51B ASP* 2.9 26.2 + - - +
65B SER* 4.6 3.3 + - - -
68B ASN* 4.7 6.6 - - - +
69B ILE* 3.4 28.0 + - - +
73B PHE* 3.6 27.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ILE* 2.9 42.5 + - + +
47B SER* 1.3 78.2 + - - +
49B ASN* 1.3 63.1 + - - +
51B ASP* 3.2 8.8 + - - -
53B ASN* 3.0 47.8 + - + +
65B SER* 4.3 15.7 - - - +
69B ILE* 5.2 1.6 - - + -
85B MET* 4.5 11.9 - - - +
99B VAL* 4.6 7.6 - - - -
121B ALA* 3.8 8.7 - - + +
122B ARG* 3.5 40.4 - - - +
123B LEU* 3.6 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LEU 3.0 10.6 + - - +
46B TYR* 3.6 7.3 + - - +
48B MET* 1.3 78.4 - - - +
50B LYS* 1.3 66.9 + - - +
52B SER* 3.0 17.0 + - - -
53B ASN 4.5 2.2 - - - +
54B THR* 4.0 14.7 - - - +
123B LEU* 3.4 9.6 - - + +
128B GLY* 5.8 1.6 - - - -
131B LEU* 3.2 47.5 - - + +
134B ILE* 4.7 11.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B TYR* 2.8 44.5 + - + +
47B SER* 3.6 4.6 + - - +
49B ASN* 1.3 76.6 - - - +
51B ASP* 1.3 61.4 + - - +
52B SER* 3.0 7.4 + - - -
72B ASN* 3.5 26.5 - - - +
73B PHE* 4.4 6.8 - - + -
149B GLU* 3.0 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B SER* 2.9 17.8 + - - +
48B MET* 3.2 6.2 + - - +
50B LYS* 1.3 77.8 - - + +
52B SER* 1.3 69.6 + - - +
53B ASN* 3.2 7.8 + - + +
68B ASN* 6.1 6.5 - - + -
----------------------------------------------------------
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