Contacts of the strand formed by residues 162 - 167 (chain C) in PDB entry 1LNU
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 TYR 162 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C LEU* 4.2 16.6 - - + -
122C TRP* 5.3 2.0 - - + -
123C LEU 3.0 7.2 - - - +
124C ARG* 3.4 47.7 + - + -
125C ASN 5.3 0.2 - - - -
152C LEU* 4.2 20.4 - - + -
154C PHE* 3.0 48.8 - + - +
155C ILE 3.6 9.6 + - - -
156C PRO* 5.8 0.7 - - + -
160C ASP* 4.1 20.0 + - - -
161C ILE* 1.3 81.5 - - - +
163C ASP* 1.3 61.8 + - - +
178C HIS* 3.0 25.1 - - - -
179C TRP* 3.2 47.3 + + + +
181C PRO* 5.9 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 163 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C TRP* 4.5 1.8 - - - -
123C LEU* 2.7 51.5 + - + +
126C SER 6.1 1.1 - - - +
162C TYR* 1.3 76.8 - - - +
164C CYS* 1.3 64.3 + - - +
176C LEU* 2.9 40.8 - - + +
177C LYS 3.0 28.3 + - - +
178C HIS* 3.1 26.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 164 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C ALA* 5.5 0.4 - - - -
92C VAL* 3.7 10.1 - - + -
108C CYS* 2.0 49.6 - - - -
120C ILE* 3.7 21.8 - - - -
121C THR 3.8 4.3 - - - -
122C TRP* 3.4 23.0 - - + -
163C ASP* 1.3 70.3 - - - +
165C LYS* 1.3 57.4 + - - +
166C VAL* 3.9 7.8 + - - +
175C VAL* 3.5 5.9 - - - +
176C LEU* 3.8 1.7 - - - -
177C LYS* 3.0 31.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 165 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C ASN 3.4 1.6 - - - +
120C ILE* 3.2 6.1 - - - +
121C THR* 2.6 63.0 + - - +
123C LEU* 3.8 27.8 - - + +
128C SER* 5.8 0.7 - - - +
163C ASP 3.4 0.6 + - - -
164C CYS* 1.3 71.1 - - - +
166C VAL* 1.3 62.6 + - - +
167C GLU* 4.6 14.7 - - + +
174C PRO* 3.6 32.2 - - + +
175C VAL 3.8 2.7 - - - -
176C LEU* 4.0 18.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 166 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C PRO* 4.2 17.3 - - + +
89C GLN 5.3 1.3 - - - +
90C ALA* 4.9 7.6 - - + -
110C VAL* 4.2 21.8 - - + -
118C ILE* 3.8 21.5 - - + -
119C ASN 3.3 1.6 - - - -
120C ILE* 3.9 23.3 - - + -
164C CYS* 4.4 8.5 - - - +
165C LYS* 1.3 80.0 - - - +
167C GLU* 1.3 67.1 + - - +
171C LEU* 3.4 8.4 - - + +
174C PRO* 3.1 5.5 - - - +
175C VAL* 2.8 48.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 167 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C ILE* 3.3 5.4 - - - +
119C ASN* 3.0 56.0 + - + +
121C THR* 4.5 16.3 + - - +
165C LYS* 4.6 12.7 - - + +
166C VAL* 1.3 78.0 - - - +
168C HIS* 1.3 61.6 + - - +
171C LEU* 3.8 6.7 - - + -
174C PRO* 3.7 24.5 - - + +
305C NAG 3.6 27.3 + - + +
----------------------------------------------------------
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