Contacts of the strand formed by residues 56 - 61 (chain B) in PDB entry 1B8M
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 56 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A PHE* 4.9 4.0 - - - -
23B TRP* 3.5 13.6 - - - -
24B VAL* 3.1 30.2 + - + +
27B ARG* 4.0 32.5 - - + -
40B VAL* 3.7 30.1 - - + -
54B GLN* 4.0 15.9 - - + -
55B TYR* 1.3 89.6 - - - +
57B PHE* 1.3 61.5 + - - +
58B GLU* 4.0 18.2 - - + +
97B VAL* 4.1 15.3 - - + -
98B ARG 5.2 1.6 - - - -
99B ALA* 4.2 7.9 - - + -
113B ILE* 4.0 22.2 - - + -
115B ILE* 4.1 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A MET* 5.2 1.1 - - + -
85A SER* 4.0 24.0 + - - -
86A TYR* 3.8 51.1 + + + +
102A PHE* 4.6 4.2 - - + -
21B SER* 3.7 31.0 - - - -
22B GLY* 3.5 22.0 - - - -
23B TRP* 3.8 42.0 - + + -
56B PHE* 1.3 76.0 - - - +
58B GLU* 1.3 64.0 + - - +
59B THR* 4.4 5.4 - - - -
115B ILE* 3.8 12.4 - - - +
117B THR* 4.9 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A SER* 5.3 0.4 - - - -
20B VAL 3.6 1.4 - - - +
21B SER* 3.4 2.8 - - - -
22B GLY 3.1 31.0 + - - +
24B VAL* 3.8 21.0 - - + +
27B ARG* 2.8 47.9 + - - -
56B PHE* 4.0 8.0 - - + +
57B PHE* 1.3 81.7 - - - +
59B THR* 1.3 61.3 + - - +
60B ARG* 3.0 25.6 + - - +
115B ILE* 3.7 21.1 - - + +
116B ASP* 3.0 25.9 + - + +
117B THR* 5.1 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLN 5.8 0.2 + - - -
85A SER* 4.5 5.9 + - - -
19B ALA* 3.6 26.7 - - + -
20B VAL 3.3 3.4 - - - +
21B SER* 2.9 24.9 + - - +
57B PHE* 4.4 6.9 - - - -
58B GLU* 1.3 74.5 - - - +
60B ARG* 1.3 62.4 + - - +
116B ASP* 2.8 19.7 + - - +
117B THR* 3.6 19.1 + - - +
118B ALA* 3.2 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ALA* 2.9 9.7 - - - +
20B VAL* 2.8 36.3 + - + +
24B VAL* 3.7 28.3 - - - +
26B ASP* 4.9 5.1 + - - -
27B ARG* 3.4 14.8 - - - +
58B GLU* 3.0 30.8 + - - +
59B THR* 1.3 74.2 - - - +
61B CYS* 1.3 65.6 + - - +
92B ALA* 4.9 4.5 - - + -
116B ASP* 3.2 27.4 + - + +
118B ALA 4.8 3.1 - - - -
119B CYS* 3.9 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ASP 3.6 0.7 - - - +
20B VAL* 3.9 6.2 - - - +
60B ARG* 1.3 79.6 - - - +
62B LYS* 1.3 61.2 + - - +
63B ALA* 3.0 20.0 + - + +
90B CYS* 4.1 6.3 - - + +
91B LYS* 3.6 29.4 - - - -
92B ALA* 3.9 6.8 - - - +
119B CYS* 2.0 48.9 - - - -
----------------------------------------------------------
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