Contacts of the helix formed by residues 49 - 61 (chain A) in PDB entry 1UW9
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 PRO 49 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ARG* 3.9 25.8 - - - +
47A GLY 3.4 10.3 - - - +
48A VAL* 1.3 89.2 - - + +
50A PRO* 1.3 76.0 - - + +
51A GLU* 4.0 6.5 - - - +
52A GLU* 3.0 17.6 + - + +
53A CYS* 3.0 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A MET* 3.4 15.4 - - + +
44A PRO* 4.5 3.1 - - + -
48A VAL 3.5 4.0 - - - +
49A PRO* 1.3 83.8 - - + +
51A GLU* 1.3 70.0 + - - +
53A CYS* 4.3 4.0 - - + -
54A GLY 2.8 25.3 + - - -
87A ILE* 3.5 13.3 - - + +
97A TYR* 3.8 52.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ARG* 3.6 32.7 + - - +
25A TYR* 3.5 45.0 + - + +
49A PRO* 4.0 6.9 - - - +
50A PRO* 1.3 95.4 - - - +
52A GLU* 1.3 56.1 + - - +
54A GLY* 3.9 0.3 - - - -
55A ALA* 3.0 28.8 + - - +
87A ILE* 3.6 12.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ASP* 3.5 13.9 - - - +
20A TYR* 2.8 28.7 + - - -
21A ARG* 2.9 41.9 + - - +
48A VAL* 4.4 2.7 - - + -
49A PRO* 3.0 27.2 + - + +
51A GLU* 1.3 76.9 - - - +
53A CYS* 1.3 59.8 + - - +
55A ALA 3.3 0.3 + - - -
56A ALA* 2.8 29.1 + - - +
1480A EDO 2.8 37.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A MET* 3.7 25.1 - - - -
44A PRO* 3.9 20.9 - - + -
48A VAL* 3.9 11.2 - - + +
49A PRO 3.0 14.2 + - - +
50A PRO 3.8 4.3 - - - +
52A GLU* 1.3 74.5 - - - +
54A GLY* 1.3 64.0 + - - +
56A ALA* 3.4 7.4 + - - +
57A VAL* 3.1 27.5 + - - +
129A ALA* 4.2 9.2 - - - -
130A LEU* 3.9 29.8 - - - +
1480A EDO 6.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A MET* 3.4 15.1 - - - -
50A PRO 2.8 16.5 + - - -
53A CYS* 1.3 76.5 - - - +
55A ALA* 1.3 56.5 + - - +
57A VAL* 3.3 5.7 + - - +
58A ALA* 3.0 27.9 + - - +
84A CYS* 3.7 24.3 - - - +
99A ALA* 4.3 4.5 - - - -
101A VAL* 4.7 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A TYR* 3.7 6.3 - - - +
21A ARG* 3.4 35.4 - - + +
24A TYR* 3.4 14.6 - - + +
25A TYR* 4.0 10.3 - - + +
51A GLU 3.0 20.3 + - - +
52A GLU 3.6 3.4 - - - +
53A CYS 3.3 0.2 - - - -
54A GLY* 1.3 73.1 - - - +
56A ALA* 1.3 59.2 + - - +
58A ALA* 3.3 0.7 + - - -
59A ALA* 2.8 31.2 + - - +
84A CYS* 4.1 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A TYR* 3.5 34.7 - - + +
52A GLU 2.8 20.8 + - - +
53A CYS* 3.6 9.2 - - - +
54A GLY 3.4 0.2 - - - -
55A ALA* 1.3 70.1 - - - +
57A VAL* 1.3 65.5 + - + +
60A GLU* 3.0 29.9 + - - +
124A VAL* 4.5 0.6 - - - +
127A PHE* 5.2 12.6 - - + -
129A ALA* 5.8 4.3 - - + -
130A LEU* 6.4 0.9 - - + -
1480A EDO 4.9 5.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A PHE* 3.7 46.0 - - + -
42A MET* 4.7 5.6 - - - -
53A CYS 3.1 16.4 + - - +
54A GLY* 3.3 8.9 + - - +
56A ALA* 1.3 75.0 - - + +
58A ALA* 1.3 55.4 + - - +
61A SER* 2.7 35.0 + - - -
99A ALA* 6.2 0.7 - - + -
101A VAL* 4.6 3.1 - - + -
124A VAL* 3.4 17.3 - - + +
130A LEU* 3.9 26.5 - - + -
133A LEU* 4.3 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 4.1 6.1 - - + +
54A GLY 3.0 16.7 + - - +
55A ALA 3.3 5.1 + - - +
57A VAL* 1.3 76.0 - - - +
59A ALA* 1.3 55.6 + - - +
61A SER* 3.4 9.9 + - - -
62A SER* 2.6 31.7 + - - -
82A GLY* 4.0 11.0 - - - +
84A CYS* 3.6 27.1 - - + +
101A VAL* 3.9 20.2 - - + +
103A TYR* 4.6 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A TYR* 3.4 31.4 - - + -
24A TYR* 3.5 31.6 - - + -
55A ALA 2.8 17.3 + - - +
56A ALA 3.7 1.1 - - - +
58A ALA* 1.3 77.8 - - - +
60A GLU* 1.3 57.4 + - - +
61A SER 3.2 0.2 - - - -
62A SER 3.1 2.6 + - - -
63A THR 3.1 11.8 + - - -
64A GLY* 2.9 25.7 + - - +
177B LYS* 3.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A TYR* 2.7 30.0 + - + +
56A ALA 3.0 19.0 + - - +
59A ALA* 1.3 75.2 - - - +
61A SER* 1.3 55.7 + - - +
62A SER 3.5 1.1 - - - -
64A GLY 3.4 18.2 - - - +
65A THR* 3.2 12.0 - - - -
66A TRP 3.5 0.2 + - - -
119A SER 4.8 1.0 - - - +
123A ASN* 4.6 11.3 + - - +
124A VAL* 3.9 11.6 - - + +
127A PHE* 3.3 36.4 - - + -
177B LYS* 3.5 20.1 + - - -
204B GLU* 5.0 0.5 - - - +
334B LYS* 3.0 28.8 + - - -
1477B CAP 3.3 10.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A VAL* 2.7 21.0 + - - -
58A ALA 3.4 3.3 + - - -
59A ALA 3.2 0.2 - - - -
60A GLU* 1.3 77.3 - - - +
62A SER* 1.3 57.2 + - - +
103A TYR* 2.6 42.1 + - - -
107A LEU* 5.1 0.5 - - - +
119A SER* 3.1 43.2 - - - -
120A ILE* 4.2 5.2 - - - -
124A VAL* 4.0 10.1 - - - -
177B LYS* 4.8 0.7 - - - +
205B ASN* 4.6 5.6 - - - -
----------------------------------------------------------
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