Contacts of the strand formed by residues 95 - 102 (chain A) in PDB entry 2ZB8
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 95 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 3.9 12.8 - - + -
79A ILE* 5.3 0.9 - - + -
80A GLY 3.5 12.8 - - - +
81A ILE* 4.1 24.0 - - + -
93A GLY 3.7 10.3 + - - -
94A ASP* 1.3 71.2 - - - +
96A VAL* 1.3 64.0 + - - +
116A LYS* 3.4 4.0 - - - +
117A VAL* 3.0 48.5 + - + +
119A PRO* 3.4 28.7 - - + -
126A LEU* 3.4 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A VAL* 4.4 2.5 - - + -
79A ILE* 3.3 7.2 - - - +
80A GLY 2.8 35.2 + - - +
82A ILE* 3.9 25.6 - - + -
90A LEU* 3.9 28.7 - - + -
94A ASP* 4.6 0.7 - - + +
95A PHE* 1.3 81.5 - - - +
97A THR* 1.3 61.3 + - - +
101A TRP* 3.6 20.1 - - + -
114A LEU* 4.0 22.7 - - + -
115A GLU 3.3 16.6 - - - +
116A LYS* 4.1 3.1 - - + -
117A VAL* 4.6 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLY* 5.8 0.2 - - - -
78A GLY 2.7 21.5 + - - -
79A ILE* 3.3 20.0 - - - +
96A VAL* 1.3 74.9 - - - +
98A SER* 1.3 66.5 + - - +
99A PHE* 6.0 4.2 - - + -
101A TRP* 3.9 3.8 - - - -
113A SER 4.3 0.2 - - - +
114A LEU* 3.7 2.9 - - - -
115A GLU* 3.0 46.6 + - + +
117A VAL* 3.6 14.4 - - + -
129A PHE* 5.3 1.6 + - + -
130A LEU* 4.5 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLY 3.5 1.6 - - - +
77A GLY* 3.4 1.0 - - - -
78A GLY 3.1 25.9 + - - -
97A THR* 1.3 83.4 + - - +
99A PHE* 1.3 64.4 + - - +
100A TYR* 3.0 27.0 + - - +
101A TRP* 3.8 13.7 + - - -
109A LEU* 5.0 4.0 - - - +
113A SER* 3.5 24.6 + - - -
114A LEU* 3.9 13.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ARG* 5.9 0.3 + - - -
76A GLY* 3.0 22.0 - - - -
77A GLY* 3.5 8.1 + - - -
97A THR* 6.0 4.9 - - + -
98A SER* 1.3 76.5 + - - +
100A TYR* 1.3 71.9 + + + +
113A SER 5.3 0.2 + - - -
115A GLU* 5.8 4.7 - - - -
135A MET* 5.3 16.8 - - + -
290A LEU* 5.1 13.0 - - + -
293A LYS* 4.8 16.8 - - - -
296A PHE* 5.1 15.3 - + - -
800A IMN 3.8 42.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ARG* 5.0 2.7 - - - -
65A ILE* 3.8 25.0 - - + +
75A ASP* 3.4 27.3 - - - +
76A GLY 3.9 0.7 - - - +
98A SER* 3.0 15.0 + - - +
99A PHE* 1.3 92.5 - + + +
101A TRP* 1.3 62.2 + - - +
102A PRO* 3.4 9.9 - - - +
109A LEU* 5.4 2.8 - - - +
113A SER* 6.0 6.1 - - - -
800A IMN 3.0 38.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A VAL* 3.4 33.3 - - + +
43A THR* 3.0 30.3 + - + +
46A LEU* 3.9 10.8 - - + -
75A ASP* 3.0 3.8 - - - -
76A GLY 2.8 38.5 + - - +
78A GLY* 3.5 29.4 - - - +
79A ILE 4.1 0.9 - - - -
80A GLY* 3.2 33.9 - - - -
96A VAL* 3.6 29.2 - - + -
97A THR* 3.9 5.2 - - - -
98A SER* 3.8 17.0 + - - +
100A TYR* 1.3 72.8 - - - +
102A PRO* 1.3 95.0 - - + +
103A TRP* 3.6 4.0 + - - -
107A VAL* 4.5 4.9 - - + +
109A LEU* 4.7 4.0 - - + -
114A LEU* 3.9 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 4.4 1.2 - - - +
73A VAL* 4.1 21.5 - - + -
74A VAL 3.4 7.6 - - - +
75A ASP* 3.9 3.8 - - + -
100A TYR 3.4 9.2 - - - +
101A TRP* 1.3 107.6 - - + +
103A TRP* 1.3 60.5 + - - +
104A GLN* 2.7 15.1 + - + +
107A VAL* 4.1 17.2 - - + +
109A LEU* 4.1 28.9 - - + -
----------------------------------------------------------
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