Contacts of the strand formed by residues 12 - 20 (chain B) in PDB entry 5HKE
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 ASN 12 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU 3.6 2.9 - - - -
8B ASN* 2.7 32.9 + - - +
9B GLY 4.5 1.4 + - - +
11B SER* 1.3 84.3 + - - +
13B TYR* 1.3 56.8 + - - +
146B ARG* 3.3 51.2 + - + +
279B ASP* 3.7 4.0 - - - +
280B LEU* 2.8 36.5 + - + +
281B ASP* 3.2 23.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 13 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B THR* 3.2 8.5 - - - +
7B LEU* 2.8 53.3 + - + +
8B ASN* 5.5 0.3 + - - -
9B GLY* 4.2 3.1 - - - -
11B SER* 3.1 43.0 + - - -
12B ASN* 1.3 76.8 - - - +
14B PHE* 1.3 64.4 + - - +
241B VAL* 3.6 11.4 - - + +
244B ASP* 2.7 43.3 + - + +
245B ILE* 4.1 17.3 - - + -
248B PHE* 3.7 20.6 - + + -
277B CYS* 3.9 14.8 - - - -
278B TYR 3.1 7.0 - - - +
279B ASP* 3.9 22.0 - - + -
280B LEU* 4.4 4.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 14 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ALA* 5.2 0.4 - - + -
5B ILE 3.5 12.6 - - - -
6B THR* 4.3 0.9 - - + -
13B TYR* 1.3 78.4 - - - +
15B GLY* 1.3 64.5 + - - +
66B ASP* 4.9 2.0 - - + -
67B ALA 3.9 8.1 - - - -
68B ILE* 4.0 9.6 - - + -
74B GLY* 3.8 6.1 - - - -
75B MET 3.6 40.2 - - - -
76B ALA* 3.7 13.2 - - + -
142B LEU* 4.1 30.1 - - + -
144B ALA* 3.8 24.0 - - + -
248B PHE* 3.7 4.0 - - - -
278B TYR* 2.7 60.3 + + - -
280B LEU* 4.0 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 15 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ALA* 3.3 3.5 - - - +
5B ILE* 2.9 32.8 + - - +
14B PHE* 1.3 84.2 - - - +
16B ARG* 1.3 65.7 + - - +
248B PHE* 3.5 8.2 - - - -
252B LEU* 4.7 0.4 - - - -
276B ASN* 3.3 22.2 - - - -
278B TYR* 4.4 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 16 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B OCS 3.1 28.7 + - - +
3B THR 3.1 14.4 - - - +
4B ALA* 3.9 11.9 - - + -
14B PHE* 6.2 0.4 - - + -
15B GLY* 1.3 75.7 - - - +
17B ASN* 1.3 79.3 + - - +
18B LEU* 3.5 16.3 - - - +
65B PHE* 3.0 25.7 + - - +
66B ASP* 2.9 41.3 + - + +
76B ALA* 4.1 6.3 - - + +
77B GLY 2.8 22.0 + - - -
78B LEU* 3.7 10.6 - - - +
252B LEU* 3.9 9.6 - - - +
274B TYR* 3.8 10.2 - - - +
275B SER* 3.3 2.8 - - - -
276B ASN* 2.8 43.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 17 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B OCS 3.5 4.2 + - - -
3B THR* 2.8 31.0 + - - +
16B ARG* 1.3 82.4 + - - +
18B LEU* 1.3 59.7 + - - +
19B ASP* 3.6 15.5 + - - +
252B LEU* 3.0 39.3 + - - +
255B VAL* 3.8 25.1 + - - +
256B GLU* 4.0 5.8 - - - +
272B THR* 3.8 6.9 + - + -
274B TYR 3.4 3.4 - - - -
275B SER* 2.7 31.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 18 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B OCS 3.3 17.3 - - - +
16B ARG* 3.5 21.4 - - - +
17B ASN* 1.3 72.6 - - - +
19B ASP* 1.3 55.5 + - - +
20B LEU* 3.9 32.8 - - + -
26B GLU* 4.8 2.0 - - - +
65B PHE* 4.1 31.0 - - + -
77B GLY 5.5 0.4 - - - +
272B THR* 3.5 1.2 - - - -
273B VAL* 2.8 42.9 + - + +
274B TYR* 2.9 51.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B OCS 2.8 48.5 + - - +
3B THR* 4.3 0.9 + - - -
17B ASN* 3.6 9.0 - - - +
18B LEU* 1.3 73.1 - - - +
20B LEU* 1.3 71.6 + - - +
79B ASN* 4.3 2.3 + - - -
224B ARG* 4.0 5.7 + - - -
255B VAL 4.6 2.3 - - - +
257B GLN* 3.0 36.9 + - - +
270B GLU* 3.7 12.6 - - + +
271B TYR 3.3 6.1 - - - +
272B THR* 2.6 32.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LEU* 3.9 36.0 + - + -
19B ASP* 1.3 81.1 - - - +
21B ASP* 1.3 61.8 + - - +
22B PHE* 3.3 46.8 + - + +
23B SER* 5.5 1.8 - - - -
26B GLU* 6.0 0.7 - - - +
65B PHE* 5.1 10.1 - - + -
79B ASN* 3.9 19.7 - - - +
270B GLU* 4.0 8.9 - - - +
271B TYR* 2.9 35.3 + - - +
273B VAL* 4.1 5.4 - - + +
----------------------------------------------------------
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