Contacts of the strand formed by residues 164 - 178 (chain C) in PDB entry 5IXM
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 ARG 164 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C LYS 3.4 8.7 - - - +
150C GLN* 3.4 50.5 - - + +
151C PHE 4.6 8.0 + - - +
159C ASN* 4.9 15.2 + - - +
162C ALA* 4.2 10.0 + - + +
163C TYR* 1.3 77.9 - - - +
165C ALA* 1.3 59.3 + - - +
166C GLN* 3.9 16.6 - - + -
191C LYS 3.4 0.7 - - - +
192C PHE* 3.3 27.7 - - - -
193C THR* 2.8 25.6 + - - +
194C SER* 5.3 1.9 - - - +
195C VAL* 3.3 35.9 - - - +
114D LEU* 4.1 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 165 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C SER* 3.6 6.1 - - - -
149C LYS* 2.8 44.3 + - + +
164C ARG* 1.3 69.9 - - - +
166C GLN* 1.3 64.7 + - - +
167C PRO* 3.8 5.1 - - - +
168C GLN* 3.9 31.0 - - + +
190C ALA* 5.5 0.2 - - + -
191C LYS 3.6 3.8 - - - -
192C PHE* 4.4 12.8 - - + -
114D LEU* 4.1 10.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 166 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C SER* 2.9 27.4 + - - -
149C LYS 5.0 1.1 - - - +
150C GLN* 3.8 19.7 + - - +
164C ARG* 4.3 17.7 - - + -
165C ALA* 1.3 76.0 - - - +
167C PRO* 1.3 66.6 - - - +
191C LYS* 2.7 35.2 + - + +
193C THR* 4.7 11.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 167 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C LEU* 4.1 25.1 - - + -
147C SER 3.3 15.7 - - - +
148C SER* 5.2 1.6 - - - -
166C GLN* 1.3 94.0 + - - +
168C GLN* 1.3 61.6 + - - +
169C LEU* 6.2 0.2 - - + -
189C ALA 3.8 1.9 - - - +
190C ALA* 3.4 2.9 - - - +
191C LYS* 3.0 29.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 168 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C THR 3.5 2.9 - - - +
146C LEU* 3.5 4.0 - - - +
147C SER* 2.9 41.9 + - - +
149C LYS* 3.2 34.0 + - - +
165C ALA* 3.9 17.1 + - + +
167C PRO* 1.3 76.0 - - - +
169C LEU* 1.3 62.4 + - - +
170C ASP* 3.2 26.9 + - - +
186C TYR* 5.0 0.2 + - - -
188C GLN* 3.3 32.3 + - + +
189C ALA 3.6 2.5 - - - -
190C ALA* 4.0 9.2 - - + +
192C PHE* 5.3 2.3 - - - -
204C ARG* 5.3 1.1 - - - +
304C ASP* 5.4 3.8 + - - +
114D LEU* 5.4 0.9 - - - +
121D GLU* 5.0 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 169 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C ALA* 4.8 4.7 - - + -
145C THR 3.4 26.5 - - - +
146C LEU* 4.1 19.3 - - + +
167C PRO* 6.2 0.4 - - + -
168C GLN* 1.3 74.8 - - - +
170C ASP* 1.3 64.5 + - - +
171C MET* 4.2 26.0 - - + +
187C GLY 3.8 0.2 - - - +
188C GLN* 3.0 9.7 - - - +
189C ALA* 2.9 51.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 170 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C ASN* 4.1 1.6 - - - +
144C ALA* 3.3 3.8 - - - -
145C THR* 2.8 50.2 + - - +
147C SER* 5.1 5.5 + - - -
149C LYS* 5.1 3.1 + - - -
168C GLN* 3.2 23.4 + - - +
169C LEU* 1.3 72.1 - - - +
171C MET* 1.3 64.0 + - - +
172C ASN* 4.8 3.8 - - - +
186C TYR* 2.8 32.4 + - + -
187C GLY 3.6 1.6 - - - -
188C GLN* 3.3 15.9 - - - +
121D GLU* 5.2 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 171 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C TRP* 4.3 24.7 - - + -
143C ASN 3.4 4.9 - - - +
144C ALA* 4.0 11.7 - - + -
169C LEU* 4.2 25.8 - - + +
170C ASP* 1.3 79.8 - - - +
172C ASN* 1.3 63.7 + - - +
185C VAL 4.6 0.4 - - - -
186C TYR* 3.3 9.0 - - - -
187C GLY* 2.9 42.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 172 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C TRP* 3.1 8.1 - - - +
143C ASN* 2.9 52.3 + - - +
170C ASP* 4.8 2.6 - - - +
171C MET* 1.3 81.0 + - - +
173C TYR* 1.3 60.8 + - - +
174C TYR* 3.5 26.7 + - + -
184C HIS* 2.9 28.7 + - - -
185C VAL 3.5 2.9 - - - -
186C TYR* 3.4 25.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 173 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C ASN* 3.8 17.9 - - + -
142C TRP* 4.0 13.0 - + + -
172C ASN* 1.3 75.0 - - - +
174C TYR* 1.3 77.2 + - - +
175C LYS* 3.8 31.7 + - + +
183C MET 6.0 0.7 - - - -
184C HIS* 3.3 6.3 - - - -
185C VAL* 2.9 54.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 174 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C GLU 5.0 0.7 - - - +
141C ASN* 2.8 35.5 + - - +
143C ASN* 3.9 10.4 + - - -
172C ASN* 3.5 34.6 + - + -
173C TYR* 1.3 88.8 - - - +
175C LYS* 1.3 65.4 + - - +
176C ASN* 5.6 4.3 - - - +
183C MET 3.7 3.1 - - - -
184C HIS* 3.2 38.3 + + + -
30D ARG* 3.3 54.8 - - - +
34D GLN* 4.4 12.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 175 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C TYR* 3.8 28.1 + - + +
174C TYR* 1.3 78.5 - - - +
176C ASN* 1.3 68.9 + - - +
178C VAL* 3.6 31.1 - - + +
182C ASP* 3.7 0.3 - - - -
183C MET* 2.8 45.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 176 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C TYR* 5.6 3.8 - - - +
175C LYS* 1.3 82.1 + - - +
177C ASP* 1.3 77.3 + - - +
178C VAL* 3.2 7.1 + - - +
182C ASP* 3.4 25.3 - - - +
183C MET 5.3 0.9 - - - +
34D GLN* 6.1 3.0 - - - +
37D ARG* 4.0 28.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 177 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C ASN* 1.3 78.1 - - - +
178C VAL* 1.3 60.0 + - - +
179C GLY* 2.9 18.8 + - - +
180C PRO 5.8 0.2 - - - -
181C PHE 3.7 3.6 - - - -
182C ASP* 3.1 12.1 + - - -
37D ARG* 2.5 32.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 178 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C LYS* 3.6 57.9 - - + +
177C ASP* 1.3 72.3 - - - +
179C GLY* 1.3 62.1 + - - +
180C PRO* 3.4 3.5 - - - +
181C PHE* 2.9 25.9 + - - +
183C MET* 3.6 37.5 - - + -
608C C8E 5.2 0.7 - - - -
----------------------------------------------------------
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