Contacts of the strand formed by residues 116 - 121 (chain B) in PDB entry 4ZCH
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 ILE 116 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B GLN* 4.1 11.9 - - + +
46B GLY* 3.9 24.2 - - - -
47B VAL 3.5 4.9 - - - +
48B ARG* 3.5 29.2 - - + -
75B SER 3.6 2.6 - - - +
76B ARG* 3.6 0.2 - - - -
77B GLU* 2.9 55.9 + - + +
82B GLN* 4.3 1.9 + - - -
114B GLY 3.5 18.8 - - - +
115B ASP* 1.3 70.5 - - - +
117B LEU* 1.3 63.1 + - - +
118B SER* 4.0 2.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B TRP* 6.0 0.2 - - - -
45B TYR 4.3 0.2 - - - +
46B GLY* 3.3 5.0 - - - -
47B VAL* 2.9 39.4 + - - +
49B ILE* 3.7 30.1 - - + -
57B LEU* 3.6 31.4 - - + -
74B VAL* 5.0 3.8 - - + -
75B SER 3.3 9.0 - - - +
76B ARG* 4.3 6.7 - - + -
85B LEU* 3.8 5.8 - - + -
111B LEU* 3.7 32.1 - - + -
115B ASP* 3.9 8.5 - - + -
116B ILE* 1.3 75.5 - - - +
118B SER* 1.3 60.7 + - - +
137B LEU* 5.2 2.5 - - + +
139B PHE* 3.7 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B GLU* 5.1 11.7 + - - -
45B TYR 3.9 17.7 - - - -
46B GLY* 4.5 4.3 - - - -
73B VAL 3.6 0.3 - - - +
74B VAL* 3.4 8.3 - - - +
75B SER* 3.0 39.9 + - - +
82B GLN* 4.2 8.1 + - - -
116B ILE* 4.9 2.6 + - - -
117B LEU* 1.3 75.6 - - - +
119B VAL* 1.3 67.9 + - - +
120B ILE* 4.0 14.9 - - - +
137B LEU* 5.3 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B THR 4.1 0.7 - - - +
27B GLU* 4.2 3.8 - - - +
28B VAL* 3.6 30.8 + - + +
30B TRP* 3.8 23.6 - - + +
45B TYR 4.9 0.6 + - - -
59B SER* 4.1 6.3 - - - +
61B VAL* 4.2 10.5 - - + -
72B GLN* 3.8 33.0 - - + -
73B VAL 3.4 4.9 - - - +
74B VAL* 4.1 9.4 - - + -
118B SER* 1.3 77.9 - - - +
120B ILE* 1.3 61.3 + - - +
121B ILE* 4.7 1.1 - - + -
137B LEU* 3.6 40.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B VAL* 3.7 33.2 - - + -
26B THR 3.5 12.1 - - - +
27B GLU* 4.7 15.0 - - + +
72B GLN* 3.5 3.1 - - - -
73B VAL* 2.7 49.9 + - + +
75B SER* 3.4 30.5 - - - +
82B GLN* 5.0 8.1 - - + -
118B SER* 4.0 14.6 - - - +
119B VAL* 1.3 76.7 - - - +
121B ILE* 1.3 65.0 + - - +
122B PRO* 3.8 3.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B VAL* 3.6 0.3 - - - -
26B THR* 2.8 47.2 + - + +
28B VAL* 3.6 30.1 - - + -
61B VAL* 4.7 6.3 - - + -
63B PHE* 4.1 14.6 - - + -
70B MET* 4.1 7.4 - - + -
71B GLY 4.3 3.4 - - - +
72B GLN* 4.3 13.0 - - + -
119B VAL* 4.3 5.2 - - + +
120B ILE* 1.3 80.4 - - - +
122B PRO* 1.4 65.9 - - + +
123B ARG* 3.1 6.0 + - + +
126B ALA* 3.7 27.4 - - + -
128B LEU* 3.7 31.2 - - + -
----------------------------------------------------------
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