Contacts of the strand formed by residues 125 - 131 (chain C) in PDB entry 5ZR1
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 125 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C ARG* 1.3 74.1 - - - +
126C ASN* 1.3 58.4 + - - +
127C VAL* 3.9 10.3 + - + -
153C ALA 5.2 0.2 - - - -
154C ALA* 4.2 24.2 + - + -
157C GLU* 3.2 45.6 + - + -
158C GLU* 3.5 21.0 + - - -
191C PHE* 3.6 30.7 - + + -
195C PHE* 4.2 22.8 + + + +
197C LYS* 3.6 43.0 + - + +
198C ASP 2.9 11.5 + - - +
199C LEU* 4.5 2.4 - - + +
200C ALA* 2.7 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 126 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C TYR* 4.7 14.5 + - - -
118C LEU* 3.6 21.8 - - + +
119C LYS* 3.2 34.0 + - - +
120C ASP 3.8 9.8 + - - +
121C GLU* 3.4 24.1 + - - +
124C ARG* 4.0 4.4 + - - +
125C TYR* 1.3 71.3 - - - +
127C VAL* 1.3 64.0 + - - +
128C LEU 4.1 0.3 + - - -
157C GLU* 4.9 10.8 + - - +
200C ALA* 3.4 27.2 - - - +
202C VAL* 5.9 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 127 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C LEU* 3.6 6.0 - - - +
125C TYR* 5.0 11.2 - - + +
126C ASN* 1.3 79.2 - - - +
128C LEU* 1.3 61.6 + - - +
129C ILE* 4.1 5.8 + - + -
149C LYS 5.1 0.4 - - - +
150C LEU* 4.1 32.3 - - + +
153C ALA* 4.1 30.5 - - + +
154C ALA* 4.9 3.1 - - + +
157C GLU* 5.7 2.2 - - - +
191C PHE* 5.8 2.5 - - + -
199C LEU* 5.0 9.0 - - + -
200C ALA 3.4 4.0 + - - +
201C MET* 3.6 25.4 - - + +
202C VAL 3.0 25.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 128 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C ILE* 3.4 43.1 - - + +
118C LEU* 3.7 14.4 - - + +
126C ASN 4.1 0.2 + - - -
127C VAL* 1.3 73.8 - - - +
129C ILE* 1.3 63.9 + - - +
130C GLU* 3.4 30.2 + - + +
149C LYS* 5.2 6.4 - - - +
202C VAL* 3.6 31.0 - - + +
204C ASN* 4.0 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 129 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C VAL* 4.5 12.6 - - + -
128C LEU* 1.3 76.8 - - - +
130C GLU* 1.3 62.4 + - - +
131C LEU* 4.1 7.9 + - + +
146C SER* 3.5 49.6 - - - +
149C LYS* 4.1 22.2 - - + -
150C LEU* 4.3 10.8 - - + +
201C MET* 3.7 30.3 - - + -
202C VAL 2.7 14.1 + - - +
203C PHE* 3.3 19.4 - - + -
204C ASN 2.8 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 130 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C THR 5.0 3.1 - - - +
115C LYS* 5.2 3.5 - - - +
116C ILE 4.9 4.9 + - - -
128C LEU* 3.4 28.8 + - + +
129C ILE* 1.3 75.5 - - - +
131C LEU* 1.3 62.9 + - - +
132C THR* 4.2 1.6 - - + -
135C GLU* 3.2 13.7 - - - +
149C LYS* 3.7 18.6 - - - +
204C ASN* 3.4 28.7 + - + +
206C LYS* 3.1 34.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 131 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C ILE* 4.4 7.9 - - + +
130C GLU* 1.3 79.4 - - - +
132C THR* 1.3 63.0 + - - +
133C PRO* 4.6 0.2 - - - +
135C GLU* 3.6 13.7 - - + +
136C SER* 4.3 14.4 - - - +
142C MET* 3.8 36.1 - - + +
145C ARG* 4.5 14.4 - - + -
146C SER* 3.7 25.4 - - - +
149C LYS* 5.1 0.7 - - - +
203C PHE* 4.0 13.0 - - + -
204C ASN 3.0 7.7 + - - -
205C PHE* 3.5 26.8 - - + +
206C LYS* 2.9 24.5 + - - -
211C ILE* 6.0 1.4 - - + +
219C PHE* 4.1 3.4 - - + -
----------------------------------------------------------
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