Contacts of the strand formed by residues 129 - 139 (chain L) in PDB entry 1RZ7
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 THR 129 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143H LYS* 4.9 7.4 + - - +
124L GLN* 3.0 51.7 + - - +
125L LEU* 3.6 6.6 + - - -
127L SER* 3.5 13.0 + - - +
128L GLY* 1.3 86.0 - - - +
130L ALA* 1.3 61.6 + - - +
180L THR* 5.0 9.2 - - + -
181L LEU 3.7 7.9 - - - -
182L SER* 5.5 1.6 - - - -
183L LYS* 4.0 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 130 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120L PRO* 4.0 7.2 - - + -
124L GLN* 4.0 1.6 - - - -
125L LEU* 3.5 21.8 - - + -
129L THR* 1.3 74.6 - - - +
131L SER* 1.3 62.0 + - - +
132L VAL* 4.1 1.1 + - + -
179L LEU 3.6 1.4 - - - +
180L THR* 3.4 2.8 - - - -
181L LEU* 2.8 44.3 + - + +
182L SER 4.5 0.9 - - - +
183L LYS* 4.8 0.4 - - - -
186L TYR* 3.7 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 131 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H LEU* 6.1 0.2 - - - +
141H LEU* 3.7 15.3 - - - +
143H LYS* 3.4 18.4 - - - -
118L PHE 4.3 0.2 - - - +
119L PRO 4.2 1.4 - - - +
120L PRO* 3.4 21.0 - - - +
124L GLN* 2.8 35.4 + - - +
130L ALA* 1.3 73.9 - - - +
132L VAL* 1.3 62.3 + - - +
133L VAL* 4.0 3.6 + - - +
178L THR* 3.7 18.6 - - - -
179L LEU 3.3 5.2 - - - -
180L THR* 3.5 6.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 132 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117L ILE* 4.2 3.1 - - + -
118L PHE 3.6 12.3 - - - +
119L PRO* 4.5 0.2 - - + -
120L PRO* 4.2 13.5 - - + -
130L ALA 4.8 1.8 - - - +
131L SER* 1.3 76.8 - - - +
133L VAL* 1.3 64.2 + - - +
148L TRP* 3.5 29.1 - - + -
178L THR* 3.3 3.3 - - - -
179L LEU* 2.7 58.9 + - + +
181L LEU* 4.7 6.5 - - + -
186L TYR* 4.6 5.6 - - + -
192L TYR* 4.3 16.2 - - + -
209L PHE* 3.6 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 133 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H LEU* 3.8 36.1 - - + -
141H LEU* 4.4 16.6 - - + -
179H SER* 5.2 1.3 - - - -
117L ILE* 3.4 4.5 - - - +
118L PHE* 2.7 50.8 + - + +
131L SER 4.6 2.9 - - - +
132L VAL* 1.3 78.5 - - - +
134L CYS* 1.3 68.8 + - - +
135L LEU* 5.3 1.8 - - + -
148L TRP* 3.8 2.5 - - - -
176L SER* 3.9 18.8 - - - +
177L SER 3.3 7.9 - - - +
178L THR* 3.9 20.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 134 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115L VAL* 4.0 9.0 - - - -
116L PHE 3.4 3.1 - - - -
133L VAL* 1.3 76.0 - - - +
135L LEU* 1.3 61.6 + - - +
136L LEU* 3.8 20.5 - - - +
146L VAL* 4.5 3.4 - - + -
148L TRP* 3.5 19.0 - - + -
175L LEU 3.8 0.9 - - - +
176L SER* 3.6 3.3 - - - -
177L SER* 2.9 36.9 + - - +
194L CYS* 2.0 48.5 - - + -
196L VAL* 4.4 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 135 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137H ALA* 4.1 16.8 - - + -
166H PHE* 3.6 33.0 - - + -
181H VAL* 4.1 23.6 - - + -
183H THR* 5.4 0.7 - - + -
114L SER 3.4 1.0 - - - +
115L VAL* 3.2 6.9 - - - +
116L PHE* 2.7 64.1 + - + +
118L PHE* 4.1 17.7 - - + -
133L VAL* 4.2 3.1 - - + -
134L CYS* 1.3 73.4 - - - +
136L LEU* 1.3 74.8 + - - +
137L ASN* 3.9 20.2 - - - +
175L LEU 3.5 3.1 - - - +
176L SER* 4.8 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 136 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113L PRO* 3.9 10.1 - - + -
114L SER 3.4 4.9 - - - -
115L VAL* 4.5 2.0 - - + -
134L CYS* 3.8 14.8 - - - +
135L LEU* 1.3 81.9 - - - +
137L ASN* 1.3 59.8 + - - +
139L PHE* 3.5 15.8 - - + -
144L ALA* 4.1 20.6 - - + -
146L VAL* 3.7 23.6 - - + -
174L SER* 3.2 6.8 - - - -
175L LEU* 2.8 52.1 + - + +
196L VAL* 3.5 46.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 137 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162H GLY 5.6 0.2 + - - -
164H HIS* 3.1 16.1 + - - -
181H VAL* 4.8 1.9 - - - +
183H THR* 3.3 31.3 + - - +
113L PRO* 3.6 0.9 - - - +
114L SER* 2.8 42.4 + - - +
116L PHE* 4.0 15.4 - - + -
135L LEU* 3.9 19.1 - - + +
136L LEU* 1.3 73.6 - - - +
138L ASN* 1.3 86.8 + - - +
139L PHE 3.6 1.3 - - - -
174L SER* 2.9 17.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 138 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164H HIS* 2.9 35.3 + - - -
111L ALA* 4.2 5.9 - - - +
112L ALA 3.8 8.7 - - - +
114L SER* 6.0 0.2 - - - +
137L ASN* 1.3 86.1 + - - +
139L PHE* 1.3 58.0 + - - +
167L ASP* 5.0 0.3 - - - +
170L ASP* 3.3 14.9 + - - +
172L THR* 3.2 30.3 + - + +
173L TYR 3.2 6.1 + - - -
174L SER* 3.1 7.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 139 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111L ALA* 3.2 15.3 - - - +
113L PRO* 3.5 36.8 - - + -
136L LEU* 3.5 30.1 - - + -
138L ASN* 1.3 74.1 - - - +
140L TYR* 1.3 64.5 + - - +
141L PRO 3.2 20.2 - - - -
142L ARG* 3.3 29.6 - - - -
144L ALA* 4.0 13.0 - - + -
163L VAL* 4.9 2.9 - - + -
172L THR* 3.4 2.2 - - - -
173L TYR* 2.8 54.2 + - + +
174L SER 4.2 1.1 - - - -
175L LEU* 3.6 25.1 - - + -
198L HIS* 3.6 9.2 - + - +
----------------------------------------------------------
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