Contacts of the helix formed by residues 16 - 29 (chain B) in PDB entry 3U7U
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 ASP 16 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU* 3.3 3.9 - - + +
15B SER* 1.4 75.5 - - - +
17B LEU* 1.3 59.3 + - - +
18B GLU* 3.1 23.1 + - - +
19B GLN* 3.3 33.7 + - + +
20B GLN* 2.8 26.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
13B SER* 5.9 0.2 - - - +
14B LEU 4.1 9.9 - - - +
15B SER 3.2 12.9 + - - +
16B ASP* 1.3 69.5 + - - +
18B GLU* 1.4 59.4 + - - +
20B GLN* 3.5 6.4 + - + +
21B TYR* 3.1 25.8 + - - +
42B SER* 3.8 32.9 - - - +
43B ILE* 5.9 0.9 - - - +
44B GLU* 3.5 43.1 - - + +
68B GLN* 6.0 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 18 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ASP* 3.1 11.7 + - - +
17B LEU* 1.4 74.6 - - - +
19B GLN* 1.4 55.6 + - - +
21B TYR* 3.2 6.1 + - - +
22B ARG* 2.8 61.8 + - - +
47B ARG* 3.4 44.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU* 3.4 19.4 - - + +
16B ASP* 3.1 36.4 + - + +
18B GLU* 1.4 78.2 - - - +
20B GLN* 1.3 58.7 + - - +
22B ARG* 3.6 37.4 + - - +
23B ALA* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ASN* 5.9 0.7 + - - -
12B SER 4.9 0.8 + - - -
13B SER* 3.5 24.1 - - - +
14B LEU* 3.2 33.2 + - - +
16B ASP 2.8 13.2 + - - +
17B LEU* 3.5 12.6 - - + +
18B GLU 3.2 0.2 - - - -
19B GLN* 1.3 75.4 - - - +
21B TYR* 1.4 62.1 + - - +
23B ALA* 3.3 7.8 + - - +
24B LEU* 3.1 22.7 + - - +
39B GLU 5.9 0.8 + - - -
41B THR* 2.8 38.3 + - - +
42B SER* 4.0 13.5 - - - +
43B ILE* 4.6 5.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LEU 3.1 14.5 + - - +
18B GLU* 3.6 13.2 - - - +
20B GLN* 1.4 73.2 - - - +
22B ARG* 1.3 71.2 + - + +
24B LEU* 3.1 10.5 + - + +
25B ARG* 2.7 52.8 + - - +
43B ILE* 4.5 16.8 - - + +
44B GLU 6.3 0.2 - - - +
47B ARG* 3.6 55.9 - - + +
48B ASP* 2.6 40.0 + - - +
49B LEU* 4.0 10.1 - - + -
51B PHE* 4.2 5.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B GLU* 2.8 49.1 + - - +
19B GLN* 3.6 32.0 + - - +
21B TYR* 1.3 78.6 - - + +
23B ALA* 1.3 55.8 + - - +
25B ARG* 3.5 8.1 + - + +
26B LYS* 3.0 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU* 4.3 11.9 - - + -
19B GLN 3.0 19.3 + - - +
20B GLN* 3.4 9.2 - - - +
21B TYR 3.2 0.4 - - - -
22B ARG* 1.3 73.2 - - - +
24B LEU* 1.4 59.9 + - - +
26B LYS* 3.0 11.9 + - + +
27B TYR* 2.9 47.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B GLN* 3.1 14.2 + - - +
21B TYR* 3.1 11.2 + - + +
23B ALA* 1.4 72.7 - - - +
25B ARG* 1.3 63.1 + - - +
27B TYR* 3.3 1.4 + - - -
28B TYR* 3.1 48.0 + - + +
39B GLU 3.3 26.2 - - - +
40B ILE* 3.9 23.6 - - + -
41B THR 5.3 0.2 - - - +
43B ILE* 3.8 21.1 - - + -
49B LEU* 3.8 20.2 - - + -
51B PHE* 3.7 24.2 - - + -
52B LEU* 5.0 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B TYR* 2.7 49.0 + - + +
22B ARG* 3.6 12.6 - - - +
24B LEU* 1.3 78.4 - - - +
26B LYS* 1.4 61.4 + - - +
29B GLU* 3.1 61.6 + - - +
48B ASP* 3.5 21.4 + - - +
50B SER* 4.8 2.4 + - - -
51B PHE* 3.3 44.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ARG 3.0 14.5 + - - +
23B ALA* 3.0 12.7 + - + +
25B ARG* 1.4 76.1 - - - +
27B TYR* 1.3 93.4 + - + +
29B GLU* 4.4 5.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B CYS* 3.9 18.9 - - - +
5B ALA* 6.2 1.8 - - + -
6B GLY* 4.6 16.5 + - - -
7B THR* 3.6 32.4 - - + +
23B ALA* 2.9 37.2 + - + +
24B LEU* 3.9 3.6 - - - +
26B LYS* 1.3 110.5 + - + +
28B TYR* 1.3 79.7 + - + +
29B GLU 5.4 0.4 - - - -
31B CYS* 4.9 0.2 - - - +
405B SER* 5.3 9.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B CYS* 4.2 3.4 - - - -
6B GLY* 3.6 17.7 - - - -
7B THR* 3.2 19.1 + - + -
24B LEU* 3.1 38.7 + - + +
27B TYR* 1.3 87.3 - - + +
29B GLU* 1.3 66.4 + - - +
30B ASN 3.5 0.5 + - - -
31B CYS* 3.5 20.0 + - + +
34B VAL* 3.7 22.4 - - + -
37B ASN 2.6 28.4 + - - -
38B LEU* 3.7 22.7 - - + -
39B GLU 3.2 26.9 + - - -
51B PHE* 4.3 13.4 - - + +
52B LEU* 4.6 8.5 - - + +
54B SER* 3.7 7.3 + - - -
55B VAL* 4.7 5.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ARG* 3.1 56.7 + - - +
26B LYS* 4.4 5.0 + - - +
27B TYR 3.9 0.7 - - - +
28B TYR* 1.3 78.3 - - - +
30B ASN* 1.3 81.0 + - - +
31B CYS* 3.2 5.8 + - - +
51B PHE* 3.8 26.8 - - + +
----------------------------------------------------------
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