Contacts of the strand formed by residues 173 - 182 (chain C) in PDB entry 3QUM
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 173 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C GLU* 3.9 10.2 + - - +
106C ILE 5.0 0.7 + - - -
138C ASN* 2.9 21.1 + - - -
139C PHE* 3.3 35.0 + - + +
140C TYR* 4.5 12.2 - + - -
142C LYS* 3.0 56.9 - - + +
163C TRP* 6.3 0.9 - - + -
164C THR* 4.1 18.6 - - - +
165C ASP* 4.8 1.8 - - - -
166C GLN* 2.6 53.3 + - + +
171C SER 4.2 2.5 - - - -
172C THR* 1.3 80.2 + - - +
174C SER* 1.3 71.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 174 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C LEU 3.2 8.5 - - - -
137C ASN* 3.3 24.2 - - - -
138C ASN* 3.4 3.1 + - - -
139C PHE* 3.7 4.9 - - - -
163C TRP* 3.6 4.9 - - - +
164C THR* 3.1 37.7 + - - +
172C THR 4.7 1.6 + - - -
173C TYR* 1.3 87.7 + - - +
175C MET* 1.3 62.1 + - - +
165D HIS* 3.0 30.2 + - - -
167D PHE* 3.7 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 175 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C CYS 3.9 0.9 - - - +
135C PHE* 3.8 3.3 - - - -
136C LEU* 2.7 64.5 + - + +
139C PHE* 4.3 7.4 - - + -
144C ILE* 4.3 16.8 - - + -
145C ASN* 5.8 0.2 - - - -
146C VAL* 4.4 15.5 - - + +
161C ASN* 3.4 39.7 - - + +
162C SER 3.4 4.7 - - - +
163C TRP* 3.3 42.4 - - + +
174C SER* 1.3 76.7 - - - +
176C SER* 1.3 66.6 + - - +
177C SER* 4.8 2.0 - - - -
167D PHE* 3.5 7.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 176 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C VAL* 4.4 3.3 - - - +
134C CYS 3.8 6.3 + - - -
135C PHE* 4.4 1.9 - - - -
160C LEU 3.4 2.2 + - - +
161C ASN* 3.1 3.3 - - - +
162C SER* 2.4 45.1 + - - -
175C MET* 1.3 73.7 - - - +
177C SER* 1.3 63.2 + - - +
178C THR* 4.2 9.7 + - - -
167D PHE* 3.4 37.4 - - - -
179D SER* 3.9 18.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 177 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C VAL* 4.0 0.7 - - - +
134C CYS* 3.1 36.3 + - - +
136C LEU* 5.7 1.8 - - - -
146C VAL* 4.0 16.2 - - - +
148C TRP* 2.8 34.7 + - - -
159C VAL* 3.6 1.4 - - - +
160C LEU 3.1 5.2 - - - -
161C ASN* 2.5 23.9 + - - -
175C MET* 4.2 3.7 - - - -
176C SER* 1.3 74.6 + - - +
178C THR* 1.3 67.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 178 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C SER* 4.0 19.5 - - - +
132C VAL 3.2 18.8 - - - +
133C VAL* 3.5 17.6 - - + +
148C TRP* 4.4 2.2 - - - -
158C GLY 3.2 4.7 - - - +
159C VAL* 3.3 2.4 - - - -
160C LEU* 2.7 54.7 + - + +
176C SER* 4.2 5.2 + - - -
177C SER* 1.3 79.3 + - - +
179C LEU* 1.3 62.8 + - - +
180C THR* 4.2 4.7 - - - +
142D LEU* 5.1 10.7 - - + +
177D THR* 6.4 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 179 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C ALA 4.1 0.3 - - - +
131C SER* 3.0 3.7 - - - -
132C VAL* 2.8 44.6 + - + +
148C TRP* 4.2 41.5 - - + +
150C ILE* 5.6 3.8 - - + -
155C ARG* 4.2 17.9 - - - +
156C GLN 6.2 0.2 - - - -
158C GLY* 3.3 21.1 - - - +
159C VAL* 4.1 3.8 - - + +
178C THR* 1.3 72.5 - - - +
180C THR* 1.3 70.6 + - - +
181C LEU* 3.2 29.4 - - + +
192C TYR* 5.4 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 180 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C GLY* 6.5 0.2 - - - -
130C ALA 3.5 9.0 - - - +
131C SER* 2.8 20.6 + - - -
158C GLY* 2.9 22.9 + - - -
160C LEU* 4.3 10.6 - - - +
178C THR* 4.0 7.0 + - - +
179C LEU* 1.3 71.8 - - - +
181C LEU* 1.3 84.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 181 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C GLY* 5.1 0.7 - - - -
130C ALA* 2.7 38.5 + - - +
155C ARG* 3.2 29.6 - - - +
157C ASN* 5.7 2.2 - - + -
158C GLY* 4.0 5.6 - - - +
179C LEU* 3.2 32.6 + - + +
180C THR* 1.3 90.5 - - - +
182C THR* 1.3 89.2 + - + +
185C GLU* 4.9 17.7 - - + +
186C TYR* 5.5 3.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 182 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C GLY 4.9 1.6 - - - -
129C GLY* 4.7 3.8 - - - -
181C LEU* 1.3 95.2 - - + +
183C LYS* 1.3 61.6 + - - +
184C ASP* 3.1 7.2 + - - +
185C GLU* 3.0 29.2 + - + +
186C TYR* 3.4 17.2 + - - +
----------------------------------------------------------
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