Contacts of the strand formed by residues 86 - 94 (chain A) in PDB entry 5J0Z
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 ASP 86 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ASN* 6.1 1.0 - - - +
84A ALA 3.7 1.4 + - - +
85A ARG* 1.3 71.8 - - - +
87A ALA* 1.3 63.7 + - - +
105A ARG 4.2 0.2 - - - +
106A PHE* 3.3 2.2 - - - -
107A SER* 3.0 45.0 + - - +
84B ALA* 5.0 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ARG* 3.7 13.9 + - - +
86A ASP* 1.3 78.9 + - - +
88A ASP* 1.3 59.4 + - - +
89A VAL* 5.7 1.9 - - + +
104A GLU* 3.4 36.6 - - + +
105A ARG 3.4 7.2 - - - +
106A PHE* 4.1 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ALA* 1.3 73.0 - - - +
89A VAL* 1.3 69.7 + - - +
90A VAL* 3.9 1.3 - - - +
104A GLU* 3.2 6.1 - - - +
105A ARG* 3.1 46.7 + - - +
75B GLU* 5.6 2.4 - - - +
77B ARG* 3.3 31.1 - - - +
84B ALA* 5.2 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A PRO* 4.0 28.9 - - + -
87A ALA* 5.7 2.2 - - + +
88A ASP* 1.3 79.8 - - - +
90A VAL* 1.3 62.3 - - - +
91A ASP* 4.4 2.7 - - - +
92A ILE* 4.1 22.7 - - + +
102A TYR* 3.9 33.0 - - + +
103A LEU 3.9 9.0 - - - +
104A GLU* 4.3 2.2 - - + +
75B GLU* 3.5 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A PHE* 4.5 3.6 - - + -
88A ASP* 3.9 4.9 - - - +
89A VAL* 1.3 75.8 - - - +
91A ASP* 1.3 63.7 + - + +
103A LEU* 2.7 38.3 + - + +
104A GLU 3.7 2.5 - - - -
105A ARG* 3.4 36.8 - - + +
75B GLU* 3.1 39.3 - - - +
77B ARG* 3.8 20.4 - - - +
133B ARG* 3.8 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A THR* 3.4 21.7 - - - +
89A VAL* 4.0 1.3 - - - -
90A VAL* 1.3 86.4 - - + +
92A ILE* 1.3 69.6 + - - +
93A SER* 3.1 12.5 + - - -
101A GLN 3.5 3.7 - - - +
103A LEU* 2.9 35.1 + - + +
133B ARG* 5.5 4.9 - - - +
135B VAL* 4.7 8.6 - - - +
136B ASP* 2.8 26.4 - - - +
179B ARG* 3.1 13.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LYS 3.9 0.2 - - - +
65A THR* 3.2 30.8 - - - +
66A TYR* 3.4 24.9 + - + +
67A GLU 4.3 1.1 - - - +
68A PRO* 3.5 36.8 - - + +
71A ILE* 3.8 14.8 - - + -
73A ILE* 3.7 16.6 - - + -
89A VAL* 4.1 9.2 - - + -
91A ASP* 1.3 80.7 + - - +
93A SER* 1.3 59.4 + - - +
94A VAL* 4.8 3.1 - - + -
100A VAL* 3.7 28.3 - - + -
101A GLN 3.3 4.3 - - - +
102A TYR* 3.9 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A VAL* 4.7 9.2 - - - -
64A LYS 3.6 4.0 - - - -
91A ASP* 3.1 10.3 + - - -
92A ILE* 1.3 72.1 - - - +
94A VAL* 1.3 60.6 + - - +
95A SER 4.0 0.4 - - - -
100A VAL* 3.5 1.4 - - - +
101A GLN* 2.7 53.4 + - - +
136B ASP* 2.7 37.7 + - - -
179B ARG* 3.4 12.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 3.9 38.1 - - + +
54A PHE* 3.6 7.3 - - + -
63A VAL* 3.7 5.3 - - - -
64A LYS* 2.7 36.0 + - + +
66A TYR* 3.5 35.7 - - + -
71A ILE* 4.9 0.2 - - + -
92A ILE* 4.8 2.5 - - + -
93A SER* 1.3 76.1 - - - +
95A SER* 1.3 73.9 + - - +
98A GLY* 4.4 6.7 - - - -
99A THR 3.5 8.3 - - - +
100A VAL* 4.2 16.4 - - + -
----------------------------------------------------------
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