Contacts of the strand formed by residues 175 - 183 (chain H) 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 175 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110H THR* 5.2 6.1 - - + +
144H GLY 3.1 20.6 + - - -
145H TYR* 3.0 44.8 + - + +
146H PHE* 3.1 44.8 - + - -
148H GLU* 2.8 40.2 + - + +
168H ALA* 4.0 21.1 - - + -
169H VAL 3.6 3.1 - - - -
170H LEU* 3.3 37.4 - - + +
174H LEU* 1.3 75.1 - - - +
176H THR* 1.3 60.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 176 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141H LEU* 4.2 16.4 - - + -
142H VAL 3.7 8.5 - - - +
143H LYS* 3.5 34.5 + - + +
144H GLY* 4.1 0.9 + - - -
145H TYR* 4.6 0.2 - - - -
168H ALA* 3.5 1.8 - - - -
169H VAL* 2.8 36.0 + - + +
174H LEU* 4.0 2.5 + - - +
175H TYR* 1.3 73.9 + - - +
177H LEU* 1.3 70.7 + - - +
160L LEU* 5.2 13.2 - - + +
178L THR* 5.5 13.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 177 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141H LEU* 3.9 1.7 - - - +
142H VAL* 2.7 69.7 + - + +
145H TYR* 3.6 10.5 - - + +
150H VAL* 3.4 35.4 - - + +
151H THR* 5.8 0.4 - - - +
152H LEU* 5.7 6.5 - - + -
165H THR* 3.3 33.4 - - + -
166H PHE* 3.4 17.3 - - - +
167H PRO 5.7 0.2 - - - -
168H ALA* 3.9 9.6 - - + +
176H THR* 1.3 81.7 - - - +
178H SER* 1.3 56.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 178 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H LEU* 6.1 0.9 - - - -
140H CYS 3.4 15.5 - - - -
141H LEU* 4.0 15.5 - - - -
142H VAL* 5.7 0.7 - - - -
165H THR* 4.3 3.1 - - - -
166H PHE* 2.8 51.5 + - - +
177H LEU* 1.3 78.9 - - - +
179H SER* 1.3 60.0 + - - +
133L VAL* 5.6 4.6 - - - +
135L PHE* 4.1 13.2 - - - -
176L SER* 4.0 10.7 + - - -
178L THR* 6.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 179 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139H GLY 3.6 1.0 - - - -
140H CYS 3.3 27.2 + - - +
152H LEU* 3.6 20.0 - - - +
154H TRP* 3.4 22.2 + - - -
163H VAL* 4.6 0.7 - - - -
164H HIS 2.9 19.7 - - - -
165H THR* 3.1 30.1 + - - -
166H PHE* 4.5 1.3 - - - -
178H SER* 1.3 74.7 - - - +
180H SER* 1.3 61.0 + - - +
135L PHE* 4.3 4.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 180 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137H THR* 4.5 4.3 + - - -
138H LEU* 3.5 24.7 - - - -
139H GLY* 3.9 2.7 - - - -
154H TRP* 4.2 1.6 - - - -
162H GLY 4.3 0.2 - - - +
163H VAL* 3.6 5.6 - - - +
164H HIS* 3.1 29.3 + - - +
166H PHE* 5.1 0.7 - - - -
179H SER* 1.3 73.4 - - - +
181H VAL* 1.3 60.9 + - - +
182H THR* 4.3 0.3 + - - -
118L PHE* 5.9 0.7 - - - -
135L PHE* 2.6 42.2 - - - -
137L ASN* 4.2 11.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 181 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136H VAL 4.2 0.9 - - - +
137H THR* 3.8 0.2 - - - -
138H LEU* 2.9 39.4 + - + +
154H TRP* 4.0 31.2 - - + -
159H LEU* 4.0 29.6 - - + -
161H SER 4.9 0.4 - - - +
162H GLY* 3.1 20.0 - - - +
163H VAL* 4.0 12.8 - - + -
180H SER* 1.3 75.8 - - - +
182H THR* 1.3 74.7 + - - +
183H VAL* 4.2 6.1 + - + +
193H ILE* 5.3 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 182 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135H SER* 4.2 20.4 - - - -
136H VAL 3.6 9.2 - - - +
137H THR* 3.0 26.4 + - + +
161H SER 5.1 0.7 - - - +
162H GLY* 2.9 23.9 + - - +
180H SER 4.3 0.4 + - - -
181H VAL* 1.3 73.6 - - - +
183H VAL* 1.3 75.5 + - - +
137L ASN* 5.0 7.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 183 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135H SER* 4.0 4.3 - - - -
136H VAL* 2.5 49.4 + - + +
138H LEU* 5.4 3.1 - - + -
159H LEU* 4.0 27.1 - - + -
181H VAL* 4.5 8.3 - - + +
182H THR* 1.3 85.5 - - - +
184H THR* 1.3 63.1 + - + +
187H THR* 5.8 0.2 - - - +
188H TRP* 4.2 28.0 - - + +
193H ILE* 6.0 4.0 - - + -
----------------------------------------------------------
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