Contacts of the helix formed by residues 3 - 19 (chain B) in PDB entry 3A46
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 GLU 3 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B PRO* 1.3 75.6 - - - +
4B GLY* 1.3 68.8 + - - +
5B PRO* 3.3 1.3 - - - -
6B GLU* 3.0 23.8 + - - +
7B VAL* 3.1 15.9 + - - +
60B LYS* 4.2 4.9 - - - -
170B GLY 3.6 7.9 - - - +
172B GLY* 2.7 31.0 + - - -
173B ASN 3.4 1.4 + - - -
174B TYR* 2.8 46.2 + - + -
175B LEU* 3.0 29.2 + - + +
20F 3DR 3.5 10.2 - - - +
21F G 3.4 16.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 4 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B GLU* 1.3 70.4 - - - +
5B PRO* 1.3 61.2 - - - +
7B VAL* 3.3 2.1 + - - +
8B ALA* 2.9 32.5 + - - +
59B GLY* 3.5 21.7 - - - +
60B LYS* 3.9 2.4 - - - +
138B ASP* 5.8 2.5 - - - -
140B LEU* 4.9 5.2 - - - -
170B GLY* 2.6 29.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 5 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B GLU* 3.6 3.8 - - + -
4B GLY* 1.3 88.0 - - - +
6B GLU* 1.3 65.7 + - - +
8B ALA* 3.6 1.2 - - - +
9B LEU* 3.0 27.1 + - - +
140B LEU* 4.3 15.0 - - + -
170B GLY 4.1 0.9 - - - +
174B TYR* 5.2 0.2 - - - +
175B LEU* 3.6 24.2 - - + -
210B THR* 3.6 27.8 - - + +
213B ALA* 3.7 17.9 - - + +
214B TYR* 3.6 27.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 6 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B PRO* 3.4 25.8 - - + -
3B GLU* 3.0 23.0 + - - +
5B PRO* 1.3 81.8 - - - +
7B VAL* 1.3 58.0 + - - +
9B LEU* 3.4 2.2 + - - +
10B THR* 2.8 35.5 + - - +
82B PHE* 5.3 1.1 - - + -
174B TYR* 2.6 34.6 + - - -
213B ALA 5.3 0.2 - - - +
219B ILE* 3.6 23.7 - - - +
221B TYR* 4.2 15.6 - - + +
222B MET* 3.8 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 7 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B PRO* 4.5 7.0 - - + +
3B GLU 3.1 14.0 + - - +
4B GLY 3.7 6.1 - - - +
6B GLU* 1.3 75.3 - - - +
8B ALA* 1.3 63.9 + - - +
10B THR* 3.2 8.3 + - - -
11B ALA* 3.0 21.8 + - - +
57B THR* 3.6 25.3 - - + +
59B GLY 3.9 4.9 - - - +
60B LYS* 3.7 39.7 - - + +
62B LEU* 4.0 13.7 - - + +
82B PHE* 4.3 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 8 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B GLY 2.9 17.7 + - - +
5B PRO 3.6 4.0 - - - +
7B VAL* 1.3 76.6 - - - +
9B LEU* 1.3 63.8 + - - +
11B ALA* 3.1 13.7 + - - +
12B ASP* 3.1 19.4 + - - +
57B THR* 3.8 19.7 + - - +
59B GLY 5.8 0.2 - - - +
138B ASP* 6.0 0.4 - - - +
140B LEU* 3.8 23.8 - - + -
141B LYS* 5.0 7.2 - - + +
214B TYR* 4.3 5.6 - - + -
237B TYR* 5.2 3.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 9 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B PRO 3.0 18.5 + - - +
6B GLU* 3.8 2.9 - - - +
8B ALA* 1.3 75.1 - - - +
10B THR* 1.3 63.4 + - - +
12B ASP* 3.2 10.6 + - + +
13B ILE* 3.1 29.8 + - + +
214B TYR* 3.9 22.3 - - + +
216B SER 3.9 6.3 - - - +
217B ASN 6.2 0.2 - - - -
222B MET* 3.8 26.7 - - + -
229B SER* 3.9 9.9 - - - +
232B ILE* 4.5 13.0 - - + -
233B GLY 4.7 0.9 - - - +
234B ARG* 3.5 51.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 10 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B GLU* 2.8 25.8 + - - +
7B VAL 3.2 6.3 + - - -
9B LEU* 1.3 75.7 - - - +
11B ALA* 1.3 58.0 + - - +
13B ILE* 3.2 3.7 + - - +
14B LEU* 2.8 34.1 + - + +
62B LEU* 4.6 0.4 - - + -
82B PHE* 4.0 16.1 - - + -
88B TRP* 3.7 43.4 + - + +
222B MET* 3.6 23.3 - - - +
225B LEU* 3.9 11.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 11 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B VAL 3.0 5.8 + - - +
8B ALA 3.1 6.3 + - - +
10B THR* 1.3 77.1 - - - +
12B ASP* 1.3 54.9 + - - +
14B LEU* 3.1 2.5 + - - +
15B GLU* 2.8 40.5 + - - +
55B VAL* 3.9 25.3 - - + +
56B ASP* 4.5 1.3 - - - +
57B THR* 3.3 34.1 - - + +
62B LEU* 3.9 7.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 12 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ALA* 3.1 11.6 + - - +
9B LEU* 3.2 11.5 + - + +
11B ALA* 1.3 77.7 - - - +
13B ILE* 1.3 57.1 + - - +
15B GLU* 3.4 8.6 + - - +
16B LYS* 3.0 28.1 + - - +
214B TYR* 2.6 38.6 + - - -
232B ILE* 3.8 16.8 - - + +
233B GLY 5.8 1.1 - - - +
235B LYS* 3.3 31.3 + - - +
237B TYR* 4.9 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 13 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU* 3.1 18.0 + - + +
10B THR* 3.2 7.6 + - - +
12B ASP* 1.3 75.4 - - - +
14B LEU* 1.3 68.5 + - + +
16B LYS* 3.2 3.0 + - + +
17B TYR* 3.2 45.6 + - + -
90B LEU* 5.4 0.9 - - + -
222B MET* 4.0 22.4 - - + -
225B LEU* 3.9 26.9 - - + -
228B GLU* 3.9 20.2 - - + -
229B SER* 3.9 17.7 - - - +
232B ILE* 4.2 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 14 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B THR* 2.8 37.1 + - + +
11B ALA 3.6 3.6 - - - +
13B ILE* 1.3 79.0 - - + +
15B GLU* 1.3 58.3 + - - +
18B PHE* 2.8 59.3 + - + +
55B VAL* 3.9 14.3 - - + +
62B LEU* 3.9 19.1 - - + -
64B PHE* 3.8 25.6 - - + -
88B TRP* 4.0 35.9 - - + -
89B SER 5.7 2.2 - - - +
90B LEU* 6.0 1.3 - - + -
108B ALA* 5.0 1.8 - - + -
225B LEU* 5.8 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 15 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ALA 2.8 16.1 + - - +
12B ASP* 3.5 9.2 - - - +
14B LEU* 1.3 77.9 - - - +
16B LYS* 1.3 59.2 + - - +
19B LYS* 2.9 53.4 + - + +
54B ASN* 2.6 31.9 - - - +
55B VAL* 2.8 45.7 + - + +
235B LYS* 5.9 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 16 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ASP 3.0 17.4 + - - +
13B ILE* 3.2 6.2 + - + +
15B GLU* 1.3 78.6 - - - +
17B TYR* 1.3 94.4 + - + +
19B LYS 5.1 0.9 + - - +
21B LYS* 6.0 0.3 - - - -
228B GLU 5.2 1.0 + - - -
231B LYS* 3.2 35.0 + - - +
232B ILE* 3.8 25.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 17 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ILE* 3.2 31.0 + - + +
16B LYS* 1.3 114.3 + - + +
18B PHE* 1.3 89.3 + + + +
19B LYS 3.9 0.4 - - - -
21B LYS* 3.5 24.1 + - - +
90B LEU* 3.7 33.0 - - + -
106B LEU* 4.8 6.6 - - + +
228B GLU* 3.7 26.2 + - + +
231B LYS* 4.8 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 18 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU* 2.8 37.5 + - + +
17B TYR* 1.3 90.5 - + + +
19B LYS* 1.3 66.4 + - - +
20B GLY 3.1 0.7 + - - -
21B LYS* 2.8 24.5 + - + +
52B VAL* 3.5 15.7 - - + +
55B VAL* 5.5 0.7 - - + -
64B PHE* 5.4 6.5 - + + -
90B LEU* 3.6 25.4 - - + -
102B PHE* 3.4 50.3 - + + -
106B LEU* 3.7 22.7 - - + -
107B MET 3.4 22.4 - - - -
108B ALA* 3.5 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU 3.9 0.6 + - - -
15B GLU* 2.9 48.7 + - + +
16B LYS 5.6 0.9 - - - +
17B TYR 3.9 0.5 - - - -
18B PHE* 1.3 75.9 + - - +
20B GLY* 1.3 62.1 + - - +
21B LYS* 3.4 10.9 + - - +
52B VAL* 3.9 11.4 - - + +
53B SER* 2.8 34.2 + - - +
54B ASN* 3.7 11.0 + - - +
55B VAL* 5.6 0.4 - - + +
6C C 3.4 26.6 + - - +
7C C 5.8 0.9 - - - -
----------------------------------------------------------
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