Contacts of the helix formed by residues 42 - 55 (chain A) in PDB entry 1U75
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 TYR 42 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LYS* 5.2 0.9 - - - -
30A LEU* 3.8 20.7 + - + +
33A ASP* 3.2 41.1 + - + +
36A TYR* 3.5 48.5 - + + +
41A GLY* 1.3 70.8 - - - -
43A GLY* 1.3 65.4 + - - +
44A PRO 3.4 2.0 - - - -
45A VAL* 3.2 15.2 + - + +
46A LEU* 3.1 24.3 + - + +
87A ASN* 3.4 28.0 - - + -
91A PHE* 3.5 37.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 3.4 18.4 - - - +
40A ILE 5.0 0.2 + - - -
41A GLY* 3.3 1.4 - - - -
42A TYR* 1.3 78.6 - - - +
44A PRO* 1.4 66.9 - - - +
46A LEU 3.3 0.3 + - - -
47A VAL* 3.2 21.3 + - - +
115A ALA* 3.2 14.2 - - - +
119A MET* 3.5 23.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ILE* 3.7 13.9 - - + +
41A GLY 3.8 12.6 - - - +
42A TYR 3.7 2.9 - - - -
43A GLY* 1.4 86.2 - - - +
45A VAL* 1.3 63.4 + - - +
47A VAL* 3.3 2.5 + - + -
48A ARG* 3.2 18.9 + - - +
119A MET* 3.8 15.5 - - + -
177A LEU* 3.9 4.9 - - + -
178A GLY* 3.5 37.2 - - - +
195A ASN 3.5 12.1 - - - +
196A ASN* 4.9 0.4 - - - -
1001A ZNH 3.2 27.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A TYR* 4.1 17.3 - - + +
41A GLY 5.3 0.2 + - - -
42A TYR* 3.2 31.6 + - + +
44A PRO* 1.3 78.0 - - - +
46A LEU* 1.3 58.4 + - + +
48A ARG* 3.6 3.1 + - - +
49A LEU* 3.0 27.0 + - - +
84A GLY 3.4 26.2 - - - +
85A LEU* 3.8 17.8 - - + +
88A GLY* 3.9 23.5 - - - +
1001A ZNH 3.7 24.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ILE* 4.1 10.5 - - + -
30A LEU* 3.9 17.3 - - + -
42A TYR* 3.1 15.6 + - + +
43A GLY 3.5 7.6 - - - +
44A PRO 3.2 0.2 - - - -
45A VAL* 1.3 76.2 - - - +
47A VAL* 1.3 64.1 + - - +
48A ARG 3.2 0.2 - - - -
49A LEU* 3.4 7.4 + - + +
50A ALA* 3.2 22.3 + - - +
88A GLY* 3.7 33.2 - - - +
91A PHE* 3.6 29.6 - - + -
92A LEU* 4.0 19.5 - - + -
108A PHE 4.5 1.0 - - - +
111A GLY* 3.6 24.0 - - - +
112A GLY* 3.6 7.0 + - - -
115A ALA* 4.0 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLY 3.2 17.4 + - - +
44A PRO 3.6 5.6 - - - +
46A LEU* 1.3 75.2 - - - +
48A ARG* 1.3 62.3 + - - +
50A ALA* 3.4 6.5 + - - +
51A TRP* 3.2 21.7 + - - +
112A GLY* 4.2 7.6 - - - +
115A ALA* 3.6 16.2 - - + -
116A VAL* 3.8 28.3 - - + -
119A MET* 4.5 0.4 - - + -
174A ALA* 4.4 6.3 - - + -
177A LEU* 3.8 18.2 - - + -
262A PHE* 4.9 0.7 - - + -
266A PHE* 4.0 12.0 - - + -
1001A ZNH 4.1 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A PRO 3.2 13.6 + - - +
45A VAL* 3.6 5.6 - - - +
47A VAL* 1.3 79.0 - - - +
49A LEU* 1.3 57.9 + - - +
51A TRP* 3.7 6.7 - - - -
52A HIS* 3.0 34.9 + - + +
81A SER 3.5 21.0 + - - -
83A ALA 3.2 23.2 + - - -
84A GLY* 4.2 3.0 - - - -
85A LEU* 3.5 28.8 - - + +
185A SER* 5.4 1.4 - - - +
1001A ZNH 3.3 81.1 + - + +
2201A PO4 2.9 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL 3.0 17.7 + - - +
46A LEU* 3.7 8.5 - - + +
47A VAL 3.3 0.4 - - - -
48A ARG* 1.3 73.3 - - - +
50A ALA* 1.3 66.0 + - - +
51A TRP 3.1 0.2 + - - -
52A HIS* 3.2 1.6 + - - -
53A ILE* 3.1 39.2 + - + +
71A TYR* 3.5 38.4 - - + -
85A LEU* 3.9 22.4 - - + +
88A GLY 4.2 19.7 - - - -
89A PHE* 4.3 3.8 - - - +
92A LEU* 3.9 28.3 - - + -
108A PHE* 4.0 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU 3.2 10.1 + - - +
47A VAL 3.4 10.5 - - - +
49A LEU* 1.3 80.9 - - - +
51A TRP* 1.3 53.0 + - - +
53A ILE* 3.2 11.3 - - - +
54A SER* 2.7 28.1 + - - -
108A PHE 3.8 14.8 + - - +
109A SER* 4.3 3.6 - - - +
112A GLY* 3.7 20.2 - - - +
266A PHE* 3.9 11.7 - - + -
270A LEU* 3.2 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A VAL 3.2 6.5 + - - +
48A ARG 3.7 5.6 - - - -
49A LEU 3.1 0.8 - - - -
50A ALA* 1.3 78.7 - - - +
52A HIS* 1.3 65.0 + + - +
53A ILE 3.3 0.4 - - - -
54A SER 3.3 0.2 + - - -
55A GLY* 2.6 47.1 + - - -
144A LEU* 4.5 5.6 - - + -
145A PRO* 3.9 24.5 - - + -
157A PHE* 4.1 4.9 - + - -
158A PHE* 3.8 34.1 - + - -
161A LEU* 4.2 7.2 - - + -
266A PHE* 4.6 0.9 - - + -
269A LEU* 3.7 30.1 - - + -
1001A ZNH 3.2 59.7 + + + -
2201A PO4 1.4 47.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ARG* 3.0 25.0 + - + +
49A LEU 3.2 1.1 + - - +
51A TRP* 1.3 87.7 - + - +
53A ILE* 1.3 58.6 + - + +
55A GLY 4.0 0.4 - - - -
56A THR* 3.2 24.8 - - - +
71A TYR* 6.3 0.4 - - + -
76A GLU* 4.3 2.5 - - - +
81A SER* 3.1 24.6 + - - -
82A ASN* 2.7 29.6 + - - +
85A LEU* 3.6 15.2 - - + +
144A LEU* 3.8 27.7 - - + +
2201A PO4 2.6 55.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LEU* 3.3 22.2 - - + +
50A ALA* 3.2 14.6 - - - +
52A HIS* 1.3 76.4 - - + +
54A SER* 1.3 63.5 + - - +
56A THR* 3.5 14.2 + - - +
65A GLY 3.0 23.8 - - - +
66A SER* 3.8 31.0 - - - +
69A GLY* 6.1 2.2 - - - -
71A TYR* 3.9 35.4 - - + -
76A GLU* 3.9 10.6 - - - +
105A GLY 4.3 3.8 - - - +
108A PHE* 3.6 32.3 - - + -
109A SER* 4.2 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ALA 2.7 23.1 + - - -
51A TRP* 3.8 2.9 - - - -
53A ILE* 1.3 77.3 - - - +
55A GLY* 1.3 55.2 + - - +
56A THR 3.1 10.0 + - - -
57A TRP* 3.5 20.5 + - - +
65A GLY* 4.0 1.1 - - - -
66A SER* 3.6 25.0 - - - +
161A LEU* 4.2 3.6 - - - +
269A LEU* 3.3 34.1 - - - +
270A LEU* 3.3 13.9 - - - +
272A ASN* 5.5 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A TRP* 2.6 41.6 + - - -
52A HIS 4.0 0.4 - - - -
53A ILE 3.6 0.6 - - - -
54A SER* 1.3 70.1 - - - +
56A THR* 1.3 57.6 + - - +
57A TRP 3.3 4.5 - - - -
143A ARG 3.8 7.4 - - - +
144A LEU* 4.1 9.2 - - - +
157A PHE* 4.0 7.6 - - - -
160A ARG* 2.9 19.0 + - - -
161A LEU* 4.1 9.4 - - - +
269A LEU* 4.6 0.2 - - - -
----------------------------------------------------------
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