Contacts of the strand formed by residues 155 - 158 (chain C) in PDB entry 4IZ5
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 LEU 155 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C ASP* 3.3 2.7 - - - -
112C LEU* 2.9 50.4 + - + +
133C ILE* 3.7 32.8 - - + -
150C LEU* 4.7 11.2 - - + -
151C LYS 3.4 15.0 - - - +
152C PRO* 3.0 7.2 + - + +
153C SER 3.4 0.8 - - - -
154C ASN* 1.3 85.0 - - - +
156C LEU* 1.3 62.9 + - - +
157C LEU* 3.8 3.4 + - - +
163C LEU* 4.1 16.6 - - + -
164C LYS 3.7 2.7 - - - -
165C ILE* 3.7 31.0 - - + -
217C ILE* 4.0 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 156 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C LYS* 5.3 4.5 - - - +
84C ILE* 4.2 15.9 - - + -
105C GLN* 5.2 4.9 - - - +
106C ASP 5.6 0.4 - - - +
108C MET* 3.5 37.9 - - + +
110C THR 3.5 5.6 - - - +
111C ASP* 4.0 21.1 - - + +
153C SER 4.6 4.0 - - - +
155C LEU* 1.3 72.1 - - - +
157C LEU* 1.3 60.3 + - - +
163C LEU* 3.4 3.3 - - - -
164C LYS* 2.8 43.7 + - + +
166C CYS* 3.7 38.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 157 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C MET* 3.6 7.8 - - - +
109C GLU 3.1 7.8 + - - -
110C THR* 2.7 48.4 + - + +
111C ASP 3.5 9.9 - - - +
112C LEU* 3.5 37.2 - - + +
115C LEU* 4.3 11.4 - - + -
129C PHE* 3.7 26.0 - - + -
155C LEU 3.9 3.8 - - - +
156C LEU* 1.3 74.4 - - - +
158C ASN* 1.3 67.8 + - - +
162C ASP 3.3 6.5 - - - +
163C LEU* 3.6 39.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 158 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C LEU 4.1 5.5 + - - -
108C MET* 3.4 34.8 - - - +
109C GLU* 3.3 30.9 + - + +
110C THR* 5.2 2.0 - - - -
157C LEU* 1.3 77.7 - - - +
159C THR* 1.3 54.0 + - - +
160C THR* 3.0 22.7 + - + +
161C CYS* 2.8 31.5 + - - -
162C ASP* 3.4 18.6 + - - +
----------------------------------------------------------
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