Contacts of the helix formed by residues 1 - 19 (chain B) in PDB entry 2K0F
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 ARG 1 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLU* 6.3 0.6 - - - +
7A GLU* 2.6 43.5 + - - +
120A MET* 6.1 1.2 - - - +
123A GLU* 2.8 38.2 + - - +
2B ARG* 1.3 60.2 + - + +
3B LYS 3.5 2.0 - - - +
4B TRP* 3.2 16.2 + - - +
5B GLN* 2.8 62.1 + - + +
9B HIS* 5.2 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 2 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLU* 3.5 38.4 + - - +
6A ALA* 3.6 22.5 - - - +
7A GLU* 4.4 25.7 + - + +
10A GLU* 5.0 17.4 - - + +
1B ARG* 1.3 81.4 - - + +
3B LYS* 1.3 62.3 + - + +
5B GLN* 4.5 1.3 - - - +
6B LYS* 3.4 25.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 3 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLU* 5.9 1.1 - - - -
105A MET* 3.6 8.2 - - + +
110A GLU* 2.8 30.8 + - - +
112A LEU* 3.8 5.5 - - + +
116A GLU* 2.5 49.0 + - + +
120A MET* 3.5 27.1 - - + +
1B ARG 3.5 0.8 - - - -
2B ARG* 1.3 73.7 - - + +
4B TRP* 1.3 64.5 + - - +
6B LYS* 3.6 22.0 - - + +
7B THR* 3.1 19.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 4 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A PHE* 4.0 26.5 - + - -
96A ILE* 5.7 5.4 - - + -
101A LEU* 3.7 36.8 - - + -
105A MET* 4.6 2.7 - - + -
120A MET* 2.6 54.9 + - + -
121A ILE* 4.1 1.8 - - + -
123A GLU* 4.8 7.2 - - + -
124A ALA* 3.6 16.8 - - + +
132A VAL* 4.5 10.8 - - + -
137A PHE* 5.3 2.0 - + - -
140A MET* 3.7 47.8 - - + -
141A MET* 4.1 10.0 - - + +
1B ARG* 3.2 19.8 + - - +
3B LYS* 1.3 75.8 - - - +
5B GLN* 1.3 62.9 + - + +
7B THR* 3.3 8.0 - - - -
8B GLY* 2.8 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 5 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLU* 3.4 24.5 - - + +
140A MET* 3.0 38.0 + - - +
141A MET* 4.3 13.1 - - - +
142A THR 5.9 0.2 + - - -
1B ARG* 2.8 57.1 + - + +
2B ARG 3.8 0.4 + - - +
3B LYS 3.4 0.2 - - - -
4B TRP* 1.3 74.8 - - - +
6B LYS* 1.3 51.0 + - - +
8B GLY* 3.5 2.6 - - - +
9B HIS* 2.9 54.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 6 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLU* 4.2 5.3 + - + +
10A GLU* 2.7 49.7 + - + +
11A ALA* 3.2 41.5 - - - +
13A SER* 5.7 1.6 - - - -
14A LEU* 3.9 25.7 - - - +
110A GLU* 2.8 30.6 + - + +
2B ARG 3.4 20.3 + - - +
3B LYS* 3.6 25.6 - - + +
5B GLN* 1.3 70.3 - - - +
7B THR* 1.3 64.4 + - - +
10B ALA* 3.2 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 7 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 3.9 13.5 - - - +
88A PHE* 3.8 28.9 - - + -
104A VAL* 4.6 2.9 - - + -
105A MET* 3.4 22.0 - - + -
108A LEU* 3.6 23.3 - - + -
3B LYS 3.1 14.2 + - - -
4B TRP 3.3 10.3 - - - -
6B LYS* 1.3 76.7 - - - +
8B GLY* 1.3 59.8 + - - +
10B ALA* 3.6 1.7 - - - +
11B VAL* 2.8 31.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 8 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A MET* 3.8 25.4 - - - -
4B TRP 2.8 16.1 + - - -
5B GLN* 3.0 5.7 + - - -
7B THR* 1.3 74.8 - - - +
9B HIS* 1.3 61.3 + - - +
10B ALA 3.1 1.3 - - - -
11B VAL* 4.1 2.2 - - - -
12B ARG* 3.1 38.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 9 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A GLN* 6.0 0.4 - - - -
7A GLU* 3.1 57.0 + - + -
8A PHE* 3.2 44.1 - + + -
11A ALA* 3.7 12.8 - - + -
64A PHE* 3.5 14.6 - - + -
68A MET* 3.3 27.9 - - + +
1B ARG* 5.2 0.4 + - - -
5B GLN* 2.9 31.1 + - + +
8B GLY* 1.3 72.8 - - - +
10B ALA* 1.3 57.8 + - - +
12B ARG* 5.3 2.0 - - - +
13B ALA* 3.6 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 10 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ALA 4.2 4.3 - - - +
14A LEU* 4.2 14.4 - - + -
15A PHE* 3.5 30.5 - - + +
64A PHE* 4.8 0.9 - - - -
108A LEU* 5.2 8.3 - - + -
6B LYS 3.2 18.9 + - - +
7B THR* 3.7 7.9 - - - +
8B GLY 3.1 1.0 - - - -
9B HIS* 1.3 76.7 - - - +
11B VAL* 1.3 62.9 + - - +
13B ALA* 3.1 20.4 + - - +
14B ILE* 3.2 7.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 11 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLU 4.8 0.6 - - - +
84A ALA* 3.7 30.0 + - + -
87A VAL* 3.6 43.3 - - + -
88A PHE* 4.7 13.0 - - + -
104A VAL* 6.0 0.7 - - + -
108A LEU* 5.7 5.4 - - + -
141A MET* 5.1 0.7 - - + -
7B THR* 2.8 26.6 + - + +
8B GLY* 3.9 10.3 - - - +
10B ALA* 1.3 73.3 - - - +
12B ARG* 1.3 62.6 + - - +
13B ALA 3.2 0.2 - - - -
14B ILE* 3.4 20.4 + - + +
15B GLY* 3.1 17.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 12 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A MET* 4.0 8.4 - - + +
77A SER* 4.0 12.7 + - - -
80A GLU* 2.7 60.5 + - + +
81A ILE* 3.4 30.8 - - - +
84A ALA* 4.4 9.0 - - + -
141A MET* 3.6 32.4 - - - +
142A THR 3.8 13.3 - - - +
8B GLY* 3.1 22.6 + - - +
9B HIS* 4.9 2.2 - - - +
11B VAL* 1.3 76.2 - - + +
13B ALA* 1.3 53.5 - - - +
15B GLY* 3.1 1.8 + - - -
16B ARG* 2.8 39.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 13 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PHE* 4.3 6.7 - - + -
64A PHE* 4.2 9.2 - - + -
67A MET* 3.6 11.2 - - + -
68A MET* 3.6 22.9 - - - +
9B HIS 3.6 5.8 - - - +
10B ALA 3.1 13.6 + - - +
12B ARG* 1.3 75.0 - - - +
14B ILE* 1.3 61.7 + - - +
16B ARG* 3.5 14.5 - - - +
17B LEU* 3.4 28.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 14 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PHE* 4.3 13.9 - - + -
28A LEU* 5.8 0.7 - - + -
31A VAL* 4.5 11.0 - - + -
32A MET* 4.0 30.5 - - + -
35A LEU* 4.0 26.0 - - + -
47A MET* 3.9 5.6 - - - +
87A VAL* 5.5 6.5 - - + -
108A LEU* 5.1 7.4 - - + -
10B ALA 3.2 8.6 + - - +
11B VAL* 3.6 27.4 - - + +
13B ALA* 1.3 78.0 - - - +
15B GLY* 1.3 60.0 + - - +
17B LEU 3.5 0.2 + - - -
18B SER* 2.7 38.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 15 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLU 5.4 0.9 - - - -
80A GLU* 5.3 3.4 - - - -
83A GLU* 4.0 26.7 - - - -
11B VAL 3.1 10.8 + - - -
12B ARG* 3.1 7.8 + - - -
14B ILE* 1.3 76.1 - - - +
16B ARG* 1.3 57.1 + - - +
18B SER* 3.3 3.9 + - - -
19B SER* 2.9 37.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 16 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A MET* 3.1 45.0 + - - +
68A MET* 3.8 14.6 + - - +
70A ARG 5.4 1.0 + - - -
71A LYS 5.3 1.6 + - - -
72A MET* 3.5 50.3 - - + +
76A ASP* 4.8 8.1 - - - +
79A GLU 6.2 0.2 - - - -
80A GLU* 2.8 39.6 + - + +
12B ARG 2.8 19.9 + - - +
13B ALA* 3.5 19.7 - - - +
15B GLY* 1.3 77.8 - - - +
17B LEU* 1.3 70.6 + - + +
19B SER* 3.7 14.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 17 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LEU* 6.0 3.4 - - + -
47A MET* 3.5 62.6 + - + +
50A GLU* 4.0 17.5 - - + -
51A VAL* 3.9 16.8 - - + -
59A ILE* 6.0 1.6 - - + -
67A MET* 4.2 20.0 - - + -
13B ALA* 3.4 18.2 - - + +
14B ILE 3.5 1.0 + - - -
15B GLY 3.4 0.2 - - - -
16B ARG* 1.3 84.4 - - + +
18B SER* 1.3 60.9 + - - +
19B SER 5.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 18 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A MET* 5.1 0.7 - - - +
47A MET* 3.2 16.0 - - - +
14B ILE* 2.7 30.9 + - - +
15B GLY* 3.7 4.0 - - - -
16B ARG 3.2 0.2 - - - -
17B LEU* 1.3 80.0 - - - +
19B SER* 1.3 67.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ASP* 4.4 10.2 - - - +
79A GLU* 4.4 16.6 - - - -
83A GLU* 3.4 31.6 + - - +
86A ARG* 5.1 1.4 + - - -
15B GLY* 2.9 17.0 + - - -
16B ARG* 3.7 13.8 - - - +
17B LEU 5.1 0.2 - - - -
18B SER* 1.3 81.1 - - - +
----------------------------------------------------------
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