Contacts of the helix formed by residues 31 - 50 (chain B) in PDB entry 4UC5
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 SER 31 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A HIS* 3.9 2.9 - - - -
29B PRO 3.4 4.9 + - - -
30B ILE* 1.3 75.6 - - - +
32B LYS* 1.3 60.0 + - - +
33B GLU* 3.6 13.7 + - - -
34B ALA* 3.3 11.5 + - - +
35B SER* 2.7 33.3 + - - -
133B LEU* 4.3 2.9 - - - +
137B ASN* 2.8 31.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A HIS* 3.7 31.5 - - + +
5A TYR* 5.3 0.5 + - - -
31B SER* 1.3 73.4 - - - +
33B GLU* 1.3 74.0 + - + +
35B SER* 3.4 4.5 - - - -
36B GLY* 3.1 18.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B SER* 3.2 16.4 + - - +
32B LYS* 1.3 89.3 + - + +
34B ALA* 1.3 65.1 + - - +
36B GLY* 3.3 3.3 + - - -
37B LEU* 3.0 22.7 + - - +
136B ASN 4.9 3.0 - - - +
137B ASN* 3.8 21.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ILE* 3.5 23.8 - - + -
31B SER* 3.3 15.9 + - - +
33B GLU* 1.3 76.0 - - - +
35B SER* 1.3 64.0 + - - +
37B LEU* 3.1 3.6 + - - +
38B VAL* 2.9 30.9 + - - +
133B LEU* 4.3 7.0 - - + -
136B ASN* 3.7 30.3 + - + -
137B ASN* 4.0 6.8 + - - +
158B LEU* 4.6 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A HIS* 3.3 22.0 + - - -
5A TYR* 3.5 26.6 + - - -
7A THR* 3.7 15.1 - - - +
30B ILE* 3.7 14.1 - - - +
31B SER 2.7 23.3 + - - -
32B LYS 3.4 6.1 - - - -
34B ALA* 1.3 76.1 - - - +
36B GLY* 1.3 57.4 + - - +
39B HIS* 2.9 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A TYR* 4.1 21.4 - - - -
32B LYS 3.1 11.1 + - - -
33B GLU* 3.3 3.8 + - - -
34B ALA 3.3 0.2 - - - -
35B SER* 1.3 77.1 - - - +
37B LEU* 1.3 63.9 + - - +
39B HIS* 4.0 0.5 - - - +
40B ARG* 3.1 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B GLU 3.0 14.0 + - - +
34B ALA* 3.1 7.8 + - - +
36B GLY* 1.3 76.2 - - - +
38B VAL* 1.3 56.2 - - - +
40B ARG* 3.6 28.7 - - - +
41B THR* 2.6 39.7 + - - +
82B ARG* 3.9 17.5 - - - +
136B ASN* 3.5 39.7 - - - +
139B GLY* 3.6 27.1 - - - +
141B PRO* 3.6 16.8 - - + -
160B SER* 4.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A THR* 3.5 16.8 - - + -
30B ILE* 4.6 2.0 - - + -
34B ALA 2.9 22.1 + - - +
35B SER 3.7 3.1 - - - +
37B LEU* 1.3 76.3 - - - +
39B HIS* 1.3 62.1 + - - +
41B THR* 3.9 0.5 - - - -
42B ARG* 3.0 65.7 + - - +
136B ASN* 3.4 23.8 - - - +
157B ASP 3.7 14.6 - - - +
158B LEU* 4.0 11.9 - - - +
159B ILE 4.2 4.3 - - - +
160B SER* 3.6 11.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A TYR* 3.5 46.0 - + + -
6A PRO* 3.7 26.3 + - + +
7A THR* 5.0 0.7 - - - -
10A ILE* 6.0 0.4 - - - +
35B SER 2.9 18.8 + - - +
36B GLY 4.0 3.1 - - - +
38B VAL* 1.3 78.5 - - - +
40B ARG* 1.3 65.8 + - + +
42B ARG* 3.6 7.8 + - - +
43B GLN* 3.2 25.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B GLY 3.1 19.0 + - - +
37B LEU* 3.6 29.6 - - - +
39B HIS* 1.3 79.1 - - + +
41B THR* 1.3 63.8 + - - +
43B GLN* 3.2 7.3 + - - +
44B GLU* 2.8 84.1 + - + +
82B ARG* 4.1 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 2.6 29.6 + - - +
40B ARG* 1.3 77.6 + - - +
42B ARG* 1.3 58.7 + - - +
44B GLU* 3.3 11.5 + - - +
45B ILE* 2.9 42.1 + - + +
82B ARG* 4.5 3.6 + - - -
90B LEU* 4.9 8.1 - - + -
92B VAL* 4.1 9.0 - - + -
141B PRO* 3.6 28.7 - - + +
160B SER* 3.5 28.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A PRO 4.7 1.0 + - - -
7A THR* 2.9 40.6 + - - +
10A ILE* 4.3 5.1 - - - +
38B VAL* 3.0 38.0 + - - +
39B HIS* 3.9 6.8 - - - +
41B THR* 1.3 77.0 - - - +
43B GLN* 1.3 62.8 + - - +
45B ILE* 3.2 4.5 + - - +
46B SER* 2.9 22.5 + - - -
156B ALA 3.0 20.6 + - - -
157B ASP 3.9 1.8 + - - -
159B ILE 2.8 25.5 + - - -
160B SER* 3.7 20.6 - - - +
182B SER* 3.5 31.3 - - - +
183B CYS* 3.9 6.5 - - - +
184B PRO* 3.8 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B HIS* 3.2 16.9 + - + +
40B ARG* 3.2 10.8 + - + +
42B ARG* 1.3 78.8 - - - +
44B GLU* 1.3 64.4 + - + +
46B SER* 2.9 27.3 + - - -
47B ASP* 3.1 37.9 + - - +
52B ARG* 4.0 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ARG* 2.8 65.3 + - + +
41B THR* 3.7 7.3 + - - +
43B GLN* 1.3 74.1 - - + +
45B ILE* 1.3 61.6 + - - +
47B ASP* 3.4 14.5 + - - +
48B LEU* 3.4 24.8 + - - +
53B ASP* 5.3 0.7 - - - +
55B ARG* 3.4 24.8 + - - +
82B ARG* 5.3 0.2 + - - -
90B LEU* 3.4 29.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B THR* 2.9 33.3 + - + +
42B ARG 3.2 4.2 + - - +
44B GLU* 1.3 73.0 - - - +
46B SER* 1.3 66.9 + - - +
48B LEU* 3.1 7.9 + - + +
49B VAL* 2.9 29.2 + - + +
57B LEU* 4.1 28.0 - - + -
90B LEU* 3.7 15.5 - - + -
92B VAL* 4.4 4.3 - - + -
160B SER 3.7 19.3 - - - +
161B TRP* 4.0 24.5 - - + +
184B PRO* 3.6 26.2 - - + -
299B MET* 5.0 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ARG 2.9 12.8 + - - -
43B GLN* 2.9 20.4 + - - -
45B ILE* 1.3 75.3 - - - +
47B ASP* 1.3 58.2 + - - +
49B VAL* 3.1 6.2 + - - +
50B HIS* 2.9 34.0 + - - -
52B ARG* 3.2 16.9 + - - -
184B PRO* 4.4 0.6 - - - +
230B ASP* 2.8 36.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B GLN* 3.1 27.4 + - - +
44B GLU* 3.6 16.3 - - - +
45B ILE 3.1 0.2 - - - -
46B SER* 1.3 75.5 - - - +
48B LEU* 1.3 59.9 + - - +
50B HIS 3.4 0.5 + - - -
51B GLY 3.2 3.1 + - - -
52B ARG* 2.8 75.6 + - + +
53B ASP* 3.4 16.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B GLU 3.5 11.9 - - - +
45B ILE* 3.1 8.9 + - - +
47B ASP* 1.3 73.7 - - - +
49B VAL* 1.3 65.9 + - - +
50B HIS 3.4 0.3 + - - -
51B GLY* 3.4 9.4 + - - -
53B ASP* 3.4 44.7 - - + +
55B ARG* 3.4 21.5 - - + +
56B LEU 4.4 0.4 - - - -
57B LEU* 3.7 41.1 - - + +
90B LEU* 4.1 20.6 - - + -
263B LYS* 3.9 4.7 - - - +
299B MET* 3.6 32.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ILE* 2.9 27.6 + - + +
46B SER* 3.1 10.3 + - - +
48B LEU* 1.3 79.3 - - - +
50B HIS* 1.3 70.1 + - + +
184B PRO* 4.9 0.9 - - + -
230B ASP 4.1 17.9 - - - +
231B CYS 3.8 22.9 - - - +
232B HIS* 3.9 25.6 - - + -
261B THR* 2.8 34.4 + - + -
263B LYS* 3.4 11.3 - - - +
299B MET* 3.9 13.2 - - + -
----------------------------------------------------------
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 SER* 2.9 37.0 + - - +
47B ASP 3.4 0.4 + - - +
49B VAL* 1.3 87.3 + - + +
51B GLY* 1.3 59.1 + - - +
52B ARG* 3.2 37.5 + - - +
229B PRO* 2.9 32.9 + - + +
230B ASP* 3.2 9.8 + - - -
261B THR* 4.6 11.5 - - + -
263B LYS* 4.8 1.1 - - - -
----------------------------------------------------------
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