Contacts of the strand formed by residues 174 - 183 (chain L) in PDB entry 4OQT
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 174 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169H HIS* 6.0 0.4 - - - -
83L PHE* 5.9 0.9 - + - -
106L GLU* 2.8 38.9 + - - +
139L ASN* 3.0 7.7 + - - -
140L PHE* 2.8 54.6 + - + +
141L TYR* 4.0 11.4 - + - -
143L ARG* 3.5 67.6 + - + -
164L VAL* 4.4 3.8 - - + -
165L THR* 3.4 22.0 - - - +
166L GLU* 5.7 0.2 - - - -
167L GLN* 3.6 36.1 + - + +
173L THR* 1.3 74.5 - - - +
175L SER* 1.3 64.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 175 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169H HIS* 3.2 31.0 + - - -
171H PHE* 3.6 9.9 - - - -
136L LEU* 4.8 1.1 - - - -
137L LEU 3.5 9.9 - - - -
138L ASN* 3.6 4.7 + - - -
139L ASN* 3.2 18.4 + - - -
140L PHE* 3.6 3.8 - - - -
164L VAL* 3.4 6.4 - - - +
165L THR* 2.8 46.3 + - - -
174L TYR* 1.3 71.1 + - - +
176L LEU* 1.3 63.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 176 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171H PHE* 3.4 4.7 - - - -
135L CYS 3.6 0.9 - - - +
136L LEU* 3.6 3.1 - - - +
137L LEU* 2.9 50.7 + - + +
140L PHE* 4.0 19.1 - - + -
143L ARG 5.6 2.9 - - - +
145L ALA* 4.9 13.5 - - + +
147L VAL* 4.1 14.8 - - + -
162L GLU* 3.7 25.1 - - + +
163L SER 3.3 11.9 - - - +
164L VAL* 3.5 20.2 - - + -
175L SER* 1.3 77.7 - - - +
177L SER* 1.3 65.8 + - - +
178L SER 3.6 15.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 177 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171H PHE* 3.4 37.7 - - - +
184H SER* 5.0 7.9 + - - -
186H VAL* 6.4 0.2 - - - -
134L VAL* 4.6 13.5 - - - -
135L CYS 3.5 7.2 - - - -
136L LEU* 5.4 1.3 - - - -
161L GLN 3.5 2.3 - - - +
162L GLU* 3.2 3.5 - - - -
163L SER* 2.9 34.9 + - - -
176L LEU* 1.3 75.1 - - - +
178L SER* 1.3 58.6 + - - +
179L THR* 3.9 9.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 178 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134L VAL* 3.6 1.9 - - - +
135L CYS* 2.9 35.8 + - - -
137L LEU* 5.6 0.2 - - - -
147L VAL* 3.7 27.0 - - - +
149L TRP* 3.6 19.5 + - - -
160L SER* 4.5 5.9 + - - -
161L GLN 3.4 5.8 + - - -
162L GLU* 3.3 26.8 + - - +
176L LEU* 3.6 6.4 - - - +
177L SER* 1.3 70.1 - - - +
179L THR* 1.3 62.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 179 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146H LEU* 5.1 9.4 - - + -
174H VAL* 6.0 1.7 - - - +
184H SER* 5.4 1.5 + - - +
132L SER* 4.8 13.7 - - - +
133L VAL 3.3 5.6 - - - +
134L VAL* 3.4 29.6 - - + +
160L SER* 3.3 4.9 - - - -
161L GLN* 2.8 39.2 + - - +
177L SER* 3.9 13.3 + - - -
178L SER* 1.3 75.1 + - - +
180L LEU* 1.3 61.4 + - - +
181L THR* 3.8 10.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 180 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131L ALA 3.5 1.9 - - - +
132L SER* 3.5 2.9 - - - -
133L VAL* 2.7 52.8 + - + +
149L TRP* 3.5 52.8 - - + +
151L VAL* 4.5 16.6 - - + -
156L GLN* 4.2 5.6 - - + -
159L ASN* 3.2 45.1 - - - +
160L SER* 4.1 8.3 - - - -
179L THR* 1.3 72.7 - - - +
181L THR* 1.3 60.4 + - - +
182L LEU* 4.5 9.6 - - + -
193L TYR* 4.7 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 181 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148H LYS* 5.4 5.2 - - - +
176H GLN* 5.6 2.2 + - - +
130L THR* 4.3 21.5 - - + -
131L ALA 3.5 5.4 - - - +
132L SER* 4.4 12.0 + - - +
159L ASN* 3.0 26.9 + - - +
161L GLN* 5.7 0.7 + - - -
179L THR* 3.9 10.2 + - - +
180L LEU* 1.3 74.2 + - - +
182L LEU* 1.3 73.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 182 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130L THR* 3.6 5.1 - - - +
131L ALA* 2.6 51.1 + - + +
133L VAL* 5.4 2.2 - - + -
151L VAL* 5.4 5.2 - - + -
156L GLN* 5.3 2.7 - - - +
159L ASN* 3.7 21.8 - - - +
180L LEU* 4.5 14.1 - - + -
181L THR* 1.3 88.9 - - - +
183L SER* 1.3 67.1 + - - +
186L ASP* 3.8 21.8 - - - +
187L TYR* 3.8 7.9 - - + +
190L HIS* 6.0 0.2 - - + -
193L TYR* 3.5 39.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 183 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129L GLY 3.9 9.2 - - - -
130L THR* 4.7 2.2 - - - +
182L LEU* 1.3 73.3 - - - +
184L LYS* 1.3 66.7 + - - +
185L ALA* 3.6 14.3 - - - +
186L ASP* 3.0 23.1 + - - +
187L TYR* 2.9 18.1 + - - -
----------------------------------------------------------
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