Contacts of the helix formed by residues 39 - 51 (chain B) in PDB entry 3UMO
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 39 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B THR* 3.9 13.9 - - - -
10B ALA 4.2 10.3 - - - -
12B SER* 4.1 2.6 + - - -
14B ASP* 5.0 0.2 + - - -
38B GLY* 1.3 73.4 - - - -
40B GLY* 1.3 59.6 + - - -
41B GLY 3.6 1.8 - - - -
42B ILE 3.4 3.3 + - - -
43B ASN* 2.9 38.7 + - - +
256B ASP* 4.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B THR* 4.0 2.2 - - - +
39B GLY* 1.3 72.7 - - - +
41B GLY* 1.3 57.4 + - - +
43B ASN* 3.2 1.2 + - - -
44B VAL* 2.9 30.3 + - - +
137B SER* 3.3 30.4 + - - -
138B GLY* 4.3 7.7 - - - -
256B ASP* 3.7 14.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B THR* 2.8 33.2 + - - -
7B LEU 4.1 4.3 - - - -
8B THR* 3.0 12.7 + - - -
40B GLY* 1.3 73.4 - - - +
42B ILE* 1.3 61.2 + - - +
44B VAL* 3.3 3.4 + - - +
45B ALA 3.0 16.3 + - - -
137B SER* 3.1 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B THR* 2.9 14.0 + - - +
11B PRO* 3.6 31.2 - - + -
37B PRO* 3.7 28.7 - - + -
38B GLY 3.7 11.2 - - - +
39B GLY 3.4 6.5 + - - +
40B GLY 3.2 0.6 - - - -
41B GLY* 1.3 76.1 - - - +
43B ASN* 1.3 60.3 + - - +
45B ALA* 3.2 5.4 + - - +
46B ARG* 3.0 28.1 + - - +
57B ALA* 4.2 10.8 - - + -
59B PHE* 3.8 35.7 - - + -
69B LEU* 4.1 10.8 - - + -
73B LEU* 4.1 13.8 - - + +
78B VAL* 5.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PRO 3.5 11.3 + - - +
38B GLY* 4.3 1.4 - - - -
39B GLY 2.9 29.0 + - - +
42B ILE* 1.3 71.7 - - - +
44B VAL* 1.3 60.0 + - - +
46B ARG* 2.8 37.5 + - - -
47B ALA* 2.8 30.7 + - - +
253B GLY* 6.1 1.0 - - - -
256B ASP* 3.3 32.7 + - + +
294B LEU* 3.6 16.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B THR* 4.0 14.8 - - + -
40B GLY 2.9 22.7 + - - +
41B GLY* 3.5 11.2 - - - +
43B ASN* 1.3 76.1 - - - +
45B ALA* 1.3 57.6 + - - +
47B ALA* 3.3 2.6 + - - +
48B ILE* 3.0 35.1 + - + +
135B VAL* 4.2 9.9 - - + -
137B SER* 4.2 8.7 - - - +
256B ASP* 3.9 22.9 - - - +
259B VAL* 3.8 27.1 - - + -
260B GLY* 3.8 20.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B THR* 4.0 11.2 - - - +
41B GLY 3.0 13.5 + - - +
42B ILE 3.5 8.1 - - - +
44B VAL* 1.3 76.4 - - - +
46B ARG* 1.3 62.4 + - - +
48B ILE* 3.4 3.5 + - - +
49B ALA* 3.1 22.0 + - - +
55B ALA* 3.8 37.8 + - + +
57B ALA* 4.1 6.7 - - + -
78B VAL* 4.0 16.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B GLU* 5.1 8.7 + - - +
37B PRO* 3.7 36.7 + - - +
42B ILE* 3.0 16.0 + - - +
43B ASN* 2.8 42.5 + - - +
44B VAL 3.2 0.2 - - - -
45B ALA* 1.3 74.5 - - - +
47B ALA* 1.3 64.8 + - - +
49B ALA* 3.2 2.4 + - - +
50B HIS* 3.0 40.4 + - - +
73B LEU* 4.0 11.9 - - + -
76B GLU* 2.8 40.2 + - - +
78B VAL* 4.2 10.1 - - + -
292B THR 5.2 5.1 + - - -
293B ARG* 6.1 2.2 - - - +
294B LEU* 3.6 25.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ASN 2.8 16.9 + - - +
44B VAL 3.6 4.9 - - - +
46B ARG* 1.3 75.0 - - - +
48B ILE* 1.3 64.1 + - - +
50B HIS* 3.1 9.4 + - - +
51B LEU* 3.0 28.7 + - + +
256B ASP 4.0 4.5 - - - +
257B SER* 3.8 31.9 - - - +
260B GLY* 4.6 2.5 - - - -
294B LEU* 3.7 10.9 - - + +
295B CYS* 4.1 10.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ILE* 3.9 19.1 - - + -
6B THR* 5.1 0.2 - - + -
44B VAL* 3.0 32.7 + - + +
45B ALA 3.7 4.7 - - - +
46B ARG 3.2 0.2 - - - -
47B ALA* 1.3 76.7 - - - +
49B ALA* 1.3 60.9 + - - +
51B LEU* 3.1 10.2 + - - +
52B GLY 3.2 0.2 + - - -
53B GLY 3.0 23.2 + - - -
54B SER 3.6 33.7 - - - +
55B ALA* 3.7 19.1 - - + +
260B GLY* 3.5 28.3 - - - +
263B THR* 4.2 7.4 - - + -
264B LEU* 3.9 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ALA 3.1 12.9 + - - +
46B ARG* 3.2 10.5 + - - +
48B ILE* 1.3 77.1 - - - +
50B HIS* 1.3 66.2 + - + +
52B GLY* 3.1 14.0 + - - -
53B GLY 3.5 14.0 - - - +
54B SER* 5.4 0.9 - - - +
55B ALA 6.2 0.4 - - - +
76B GLU 4.8 6.7 - - - +
77B ASN 5.2 3.8 - - - +
78B VAL* 4.2 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ARG* 3.0 32.8 + - - +
47B ALA 3.1 8.7 + - - +
49B ALA* 1.3 80.4 - - + +
51B LEU* 1.3 61.5 + - - +
52B GLY* 3.2 1.4 + - - -
76B GLU* 5.3 5.3 + - - +
293B ARG* 5.5 7.9 - - - -
294B LEU* 3.8 34.1 - - + +
295B CYS* 3.0 30.3 + - - +
296B SER* 4.9 3.1 - - - -
297B HIS* 3.4 22.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ALA 3.0 19.6 + - - +
48B ILE 3.1 5.8 + - - +
50B HIS* 1.3 76.7 - - - +
52B GLY* 1.3 59.0 + - - +
53B GLY 3.5 1.5 + - - -
257B SER 4.7 0.2 - - - +
260B GLY 4.6 0.9 - - - -
261B ALA* 3.8 39.9 - - + +
264B LEU* 3.8 16.6 - - + +
278B PHE* 4.1 16.7 - - + -
282B ALA* 4.1 7.0 - - + -
295B CYS* 3.9 13.7 - - - -
296B SER 4.2 0.7 - - - +
297B HIS* 3.7 31.5 - - + +
300B THR* 3.6 32.8 - - + +
----------------------------------------------------------
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