Contacts of the helix formed by residues 18 - 29 (chain B) in PDB entry 5BOU
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 LEU 18 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B THR 6.0 1.8 - - - +
10B THR* 5.6 0.4 - - - -
11B ILE 3.9 14.1 - - - +
12B PHE* 3.9 20.2 - - + -
16B GLY 5.7 0.2 - - - +
17B ARG* 1.3 71.2 - - - +
19B TYR* 1.3 66.7 + - - +
20B GLN* 3.3 1.8 - - + +
21B VAL* 3.1 32.6 + - + +
22B GLU* 3.0 26.3 + - - +
122B THR* 4.1 10.8 - - + +
153B SER* 5.6 5.4 - - - +
76C LEU* 4.0 20.6 - - + +
125C ARG* 3.4 49.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ARG 6.2 0.2 - - - +
9B THR 5.8 1.1 + - - +
11B ILE* 3.8 36.5 + - + +
12B PHE 3.8 6.7 - - - -
13B SER* 3.4 30.5 - - - -
14B PRO* 3.4 22.9 - - - +
17B ARG* 3.5 3.8 + - - -
18B LEU* 1.3 72.4 - - - +
20B GLN* 1.3 62.2 + - + +
22B GLU* 3.1 7.2 + - - +
23B TYR* 2.9 66.0 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A THR* 3.6 17.9 - - - +
12A PHE* 3.0 56.7 + - - +
7B SER* 6.1 0.4 - - - -
8B ARG 5.3 0.4 - - - +
9B THR* 3.4 39.7 + - - +
18B LEU* 3.3 1.2 - - + +
19B TYR* 1.3 81.0 - - + +
21B VAL* 1.3 61.9 + - + +
23B TYR* 3.9 9.2 - - - +
24B ALA* 2.8 31.0 + - - +
128B ARG* 4.1 4.4 - - - +
129B PRO* 3.7 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LEU* 3.1 31.5 + - + +
20B GLN* 1.3 79.1 - - + +
22B GLU* 1.3 63.6 + - - +
24B ALA* 3.3 6.6 + - - +
25B LEU* 3.0 43.6 + - + +
122B THR* 3.6 31.0 - - + -
129B PRO* 4.7 4.9 - - + -
152B PRO* 4.3 5.7 - - + +
153B SER* 3.7 33.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ARG* 4.2 40.3 + - + +
18B LEU 3.0 22.8 + - - +
19B TYR* 3.4 9.0 - - - +
21B VAL* 1.3 81.4 - - - +
23B TYR* 1.3 67.7 + - + +
25B LEU* 3.4 21.3 + - - +
26B GLU* 3.1 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 3.5 32.1 - - + -
13A SER 3.4 16.4 - - - +
14A PRO* 3.7 44.1 - - + +
16A GLY* 3.4 9.5 - - - -
19B TYR* 2.9 55.2 + + + +
20B GLN* 3.9 9.2 - - - +
22B GLU* 1.3 82.4 - - + +
24B ALA* 1.3 64.6 + - - +
26B GLU* 3.2 9.3 + - + +
27B SER* 3.1 16.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 3.9 32.6 - - + -
20B GLN 2.8 19.0 + - - +
21B VAL 3.3 4.9 + - - +
23B TYR* 1.3 76.9 - - - +
25B LEU* 1.3 56.3 + - - +
27B SER* 3.2 5.5 + - - -
28B ILE* 3.1 32.7 + - - +
129B PRO* 4.4 3.4 - - + -
131B GLY* 4.4 4.1 - - - -
152B PRO* 3.9 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B VAL* 3.0 33.3 + - + +
22B GLU* 3.5 22.4 - - - +
24B ALA* 1.3 73.4 - - - +
26B GLU* 1.3 65.2 + - - +
28B ILE* 3.4 8.8 + - + +
29B SER* 3.2 22.0 + - - -
133B SER* 4.6 4.9 - - - +
151B ASN* 4.0 19.7 - - + +
152B PRO* 3.9 23.6 - - + -
153B SER* 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PRO 3.8 9.4 - - - +
15A SER* 3.4 27.5 - - - +
16A GLY* 4.2 0.7 - - - -
22B GLU 3.1 12.7 + - - +
23B TYR* 3.3 14.1 - - + +
24B ALA 3.2 0.2 - - - -
25B LEU* 1.3 75.1 - - - +
27B SER* 1.3 62.1 + - - +
29B SER* 2.7 30.0 + - - -
30B HIS* 3.1 30.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 4.1 14.7 - - - -
16A GLY* 3.2 28.0 + - - -
18A LEU* 6.0 0.2 - - - +
23B TYR 3.1 10.0 + - - -
24B ALA 3.3 10.8 - - - -
26B GLU* 1.3 77.2 - - - +
28B ILE* 1.3 63.0 + - - +
30B HIS* 3.2 25.1 + - - +
31B ALA* 3.9 3.6 + - - +
78B GLY* 5.6 2.2 - - - -
79B LEU* 4.3 17.2 - - - +
131B GLY* 5.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ALA 3.1 12.1 + - - +
25B LEU* 3.7 12.1 - - + +
26B GLU 3.3 0.4 - - - -
27B SER* 1.3 76.8 - - - +
29B SER* 1.3 57.7 + - - +
30B HIS 3.1 0.4 - - - -
31B ALA* 3.0 22.5 + - - +
77B ALA* 3.6 30.3 - - + +
78B GLY* 4.2 2.9 - - - -
131B GLY 3.8 11.7 - - - +
132B VAL 3.6 14.4 - - - +
133B SER* 3.5 29.2 - - - +
152B PRO* 3.5 30.3 - - + -
164B VAL* 5.4 0.2 - - + -
165B GLY* 3.4 18.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU 3.2 12.8 + - - -
26B GLU* 2.7 33.9 + - - -
28B ILE* 1.3 75.5 - - - +
30B HIS* 1.3 65.1 + - - +
31B ALA 3.5 0.4 - - - -
165B GLY 3.7 12.3 - - - -
166B ALA* 3.2 24.0 - - - +
167B ASN 4.6 0.5 + - - -
----------------------------------------------------------
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