Contacts of the strand formed by residues 54 - 59 (chain B) in PDB entry 5HVO
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 PHE 54 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ARG* 6.0 1.8 - - - -
13B LEU* 3.1 38.6 - - + +
15B ILE* 4.0 17.9 - - + -
47B GLY 4.0 19.3 - - - -
49B SER* 3.5 33.2 - - - -
50B LYS* 4.6 15.0 - - + -
52B THR* 3.8 17.5 - - - -
53B THR* 1.3 83.5 + - - +
55B GLN* 1.3 61.7 + - - +
56B TRP* 4.5 15.3 - + - +
81B ASN* 3.9 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ARG* 5.3 10.1 - - - +
13B LEU 3.0 6.5 + - - -
14B LEU* 3.5 19.0 - - + +
15B ILE* 2.9 24.8 + - - +
54B PHE* 1.3 74.9 - - - +
56B TRP* 1.3 63.8 + - - +
57B TYR* 3.7 23.9 - - + +
77B LYS* 5.0 9.7 - - - +
81B ASN* 2.8 41.0 + - - +
82B ALA 3.2 14.3 + - - -
83B THR* 2.6 25.3 + - - +
139B GLU* 4.0 3.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ILE* 3.4 57.0 - - + -
17B SER* 5.5 4.5 - - - -
20B LEU* 3.8 16.1 - - + +
21B PRO* 4.0 31.4 - - + -
22B ILE* 6.4 0.4 - - + -
36B MET* 5.1 12.8 - - + +
45B LEU* 3.7 39.5 - - + -
46B SER* 5.7 0.4 - - - -
47B GLY 6.0 1.1 - - - -
54B PHE* 4.5 14.5 + + + +
55B GLN* 1.3 78.7 - - - +
57B TYR* 1.3 61.6 + - - +
80B PHE 4.1 12.8 + - - -
81B ASN* 3.0 18.6 + - + -
82B ALA* 3.4 5.7 - - + -
83B THR* 2.7 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ARG* 5.4 1.0 + - - -
14B LEU* 3.2 49.4 - - + +
15B ILE 2.7 16.3 + - - +
16B VAL* 3.5 12.9 - - + +
17B SER* 3.0 28.5 + - - +
19B ARG 4.9 0.2 - - - +
20B LEU* 3.8 3.5 - - - +
55B GLN* 3.7 15.0 - - + +
56B TRP* 1.3 74.3 - - - +
58B GLY* 1.3 59.0 + - - +
83B THR* 3.5 24.9 - - + +
85B VAL* 4.9 4.3 - - + -
132B PHE* 4.6 0.7 - - - -
135B THR* 4.0 10.8 - - + -
136B ILE* 3.5 43.0 + - + -
139B GLU* 2.6 45.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B SER 3.2 15.5 - - - -
19B ARG 4.0 0.2 - - - -
20B LEU* 3.4 27.8 - - - +
57B TYR* 1.3 75.1 - - - +
59B TRP* 1.3 65.5 + - - -
83B THR 3.5 2.2 + - - -
84B PRO* 3.5 3.3 - - - +
85B VAL* 2.9 25.3 + - - +
132B PHE* 4.0 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ASN* 3.0 26.8 + - - +
19B ARG* 3.5 46.6 - - + +
20B LEU* 3.2 20.3 + - - -
58B GLY* 1.3 70.9 - - - -
60B PRO* 1.3 86.9 - - + +
61B GLY* 3.1 41.9 + - - -
62B LEU* 3.6 18.2 + - - -
85B VAL* 3.3 15.0 - - - +
87B MET* 3.7 45.2 + - + +
89B ASP* 5.2 5.6 - - - -
92B ALA* 3.8 23.6 - - + -
96B TYR* 5.5 9.4 - + + -
132B PHE* 3.9 5.8 - - + -
----------------------------------------------------------
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