Contacts of the helix formed by residues 15 - 30 (chain A) in PDB entry 2UYO
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 GLY 15 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL* 1.3 81.8 - - - +
16A THR* 1.3 65.6 + - - -
17A THR* 3.3 3.4 - - - -
18A ALA* 3.4 7.9 + - - +
19A VAL* 3.3 21.6 + - - +
136A VAL* 5.0 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLY* 1.3 72.4 - - - -
17A THR* 1.3 58.1 + - - +
19A VAL* 3.4 7.6 + - - +
20A MET* 3.0 27.5 + - - +
50A ALA* 5.6 7.0 - - + -
54A TRP* 4.6 17.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLY* 3.3 0.8 - - - -
16A THR* 1.3 77.0 - - - +
18A ALA* 1.3 64.7 + - - +
20A MET* 3.2 16.2 + - + +
21A VAL* 3.0 36.3 + - + +
187A GLY* 5.7 1.6 - - - +
191A TYR* 3.5 42.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL* 3.8 16.4 - - + -
15A GLY* 3.4 13.9 + - - +
16A THR 3.4 0.2 - - - -
17A THR* 1.3 78.4 - - - +
19A VAL* 1.3 62.5 + - - +
21A VAL* 3.5 11.0 - - - +
22A ALA* 3.1 24.1 + - - +
112A GLY* 4.8 7.4 - - - -
113A LEU* 3.9 22.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL* 3.8 17.7 - - + +
15A GLY 3.3 15.6 + - - +
16A THR* 3.7 7.6 - - - +
17A THR 3.2 0.4 - - - -
18A ALA* 1.3 76.2 - - - +
20A MET* 1.3 54.6 + - - +
22A ALA 3.2 1.6 + - - -
23A ALA* 2.8 33.1 + - - +
45A VAL* 3.5 14.5 - - + +
48A THR* 3.9 28.3 - - + +
50A ALA* 3.8 30.3 - - + +
51A GLY* 3.8 15.0 - - - +
54A TRP* 4.5 3.1 - - + -
113A LEU* 4.2 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A THR 3.0 17.6 + - - +
17A THR* 3.2 16.8 + - + +
19A VAL* 1.3 75.5 - - - +
21A VAL* 1.3 73.0 + - + +
23A ALA* 3.2 4.0 + - - +
24A ALA* 3.0 25.1 + - - +
54A TRP* 3.4 58.3 - - + +
80A MET* 4.0 23.6 - - + +
84A GLN* 5.7 2.2 - - - +
191A TYR* 5.9 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A THR* 3.0 31.8 + - + +
18A ALA* 3.5 12.1 - - - +
20A MET* 1.3 89.4 - - + +
22A ALA* 1.3 65.7 + - - +
24A ALA* 3.2 9.0 + - - +
25A ARG* 3.0 41.7 + - - +
84A GLN* 3.4 38.6 - - + +
87A ARG* 4.0 15.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ALA 3.1 18.9 + - - +
21A VAL* 1.3 79.0 - - - +
23A ALA* 1.3 56.3 + - - +
25A ARG* 3.1 28.1 + - - +
26A ALA* 2.8 25.8 + - - +
41A ALA* 3.4 15.8 - - + +
44A LEU* 5.3 1.1 - - + -
45A VAL* 3.5 22.0 - - + -
113A LEU* 4.1 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A VAL 2.8 15.5 + - - +
20A MET 3.4 9.2 - - - +
22A ALA* 1.3 72.6 - - - +
24A ALA* 1.3 57.2 + - - +
26A ALA* 3.2 5.0 + - - +
27A ALA* 2.9 29.7 + - - +
45A VAL* 3.8 12.7 - - + +
51A GLY* 4.5 12.1 - - - +
54A TRP* 3.6 33.0 - - + +
55A GLU* 4.9 2.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A MET 3.0 11.4 + - - +
21A VAL 3.4 9.2 - - - +
22A ALA 3.2 0.2 - - - -
23A ALA* 1.3 73.0 - - - +
25A ARG* 1.3 60.5 + - - +
27A ALA* 3.2 8.7 + - - +
28A GLU* 2.9 28.4 + - - +
80A MET* 4.2 18.4 - - + +
81A ARG* 3.9 12.9 - - - +
84A GLN* 3.5 31.4 - - + -
85A ALA 6.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A VAL* 3.0 33.1 + - - +
22A ALA* 3.1 31.8 + - - +
24A ALA* 1.3 75.8 - - - +
26A ALA* 1.3 58.4 + - - +
28A GLU* 3.2 4.8 + - - +
29A THR* 2.8 35.5 + - - -
36A ILE* 4.2 12.2 - - + +
38A ASP* 3.0 25.2 + - + +
41A ALA* 4.0 7.0 - - + +
84A GLN* 5.0 10.2 + - + +
85A ALA* 6.2 0.7 - - - +
87A ARG* 5.1 0.8 - - - +
88A THR* 3.5 36.6 + - - +
113A LEU* 3.3 32.3 + - - +
114A ASP* 4.0 10.6 - - - +
115A SER 5.5 0.4 - - - +
116A ARG* 6.1 1.0 - - - +
119A ARG* 4.9 3.3 - - - +
186A GLU* 4.9 11.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ALA 2.8 13.3 + - - +
23A ALA* 3.5 11.4 - - - +
25A ARG* 1.3 77.4 - - - +
27A ALA* 1.3 59.7 + - - +
29A THR* 3.3 7.1 + - - -
30A ASP* 3.1 30.5 + - - +
38A ASP 5.2 0.7 - - - -
41A ALA* 3.8 6.0 - - - +
42A LYS* 3.7 39.5 - - + +
45A VAL* 4.9 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ALA 2.9 13.3 + - - +
24A ALA* 3.2 11.9 + - - +
26A ALA* 1.3 71.0 - - - +
28A GLU* 1.3 67.6 + - - +
30A ASP* 3.4 14.6 + - - +
31A ARG* 3.5 15.1 - - - +
54A TRP 6.2 0.4 - - - +
55A GLU* 6.6 0.4 - - - -
81A ARG* 3.9 17.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ALA 2.9 14.0 + - - +
25A ARG* 3.6 8.3 - - - +
27A ALA* 1.3 74.9 - - - +
29A THR* 1.3 66.0 + - - +
31A ARG* 3.0 21.8 + - - +
33A ASP* 4.2 1.7 - - - +
34A ALA* 3.3 16.4 - - - +
35A LEU* 2.9 26.1 + - - +
36A ILE* 4.0 21.5 - - + +
81A ARG* 3.1 26.1 + - + +
85A ALA* 3.6 19.9 - - + +
287A ARG* 2.9 39.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ARG 2.8 19.9 + - - -
26A ALA* 3.7 7.2 - - - -
28A GLU* 1.3 78.4 - - - +
30A ASP* 1.3 58.1 + - - +
34A ALA* 4.2 1.6 - - - -
36A ILE* 3.7 11.9 + - - +
37A ARG* 2.8 40.3 + - + +
38A ASP* 2.8 47.0 + - - +
39A PRO* 4.6 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ALA 3.1 17.7 + - - +
27A ALA* 3.6 13.4 - - - +
28A GLU 3.1 0.6 + - - -
29A THR* 1.3 76.6 - - - +
31A ARG* 1.3 60.4 + - + +
32A PRO* 4.0 3.6 - - - +
42A LYS* 3.1 34.2 + - - -
----------------------------------------------------------
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