Contacts of the strand formed by residues 188 - 196 (chain C) in PDB entry 5F1B
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 ALA 188 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C ILE* 3.9 22.9 - - + -
38C ILE 3.4 10.5 - - - +
39C ARG* 4.0 15.7 - - + +
62C PRO* 4.2 0.4 - - - -
175C LEU* 3.5 3.8 - - - -
176C GLY* 3.0 37.7 + - - +
186C ALA* 3.6 3.9 - - - +
187C THR* 1.3 83.6 - - - +
189C LEU* 1.3 66.9 + - - +
190C VAL* 5.5 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 189 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LEU 3.7 0.5 - - - +
37C ILE* 3.4 5.5 - - - +
38C ILE* 2.9 46.1 + - + +
62C PRO* 3.8 32.1 - - + +
63C LEU* 4.1 13.7 - - + -
68C LEU* 4.0 5.6 - - + -
71C VAL* 4.0 31.9 - - + -
112C VAL* 3.8 26.5 - - + -
174C VAL 3.6 2.7 - - - +
175C LEU* 3.6 27.1 - - + -
186C ALA* 5.4 0.2 - - + -
188C ALA* 1.3 76.1 - - - +
190C VAL* 1.3 64.9 + - - +
191C ILE* 5.1 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 190 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C GLU* 4.9 7.2 - - - +
35C GLN* 3.8 33.2 - - + +
36C LEU 3.4 7.2 - - - +
37C ILE* 3.9 16.8 - - + -
110C LEU 3.4 7.4 - - - +
111C SER* 4.1 1.2 - - - -
112C VAL 4.9 0.3 + - - -
173C LEU 3.6 20.6 - - - +
174C VAL* 2.9 25.9 + - - +
175C LEU 4.1 24.0 - - - +
176C GLY* 4.5 3.4 - - - +
188C ALA* 4.9 1.1 - - + +
189C LEU* 1.3 77.9 - - - +
191C ILE* 1.3 66.3 + - - +
192C THR* 4.1 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 191 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C GLU 3.7 1.0 - - - +
35C GLN* 3.3 4.2 - - - +
36C LEU* 2.8 43.3 + - + +
38C ILE* 3.8 20.6 - - + -
71C VAL* 3.6 29.2 - - + +
74C LEU* 5.3 4.5 - - + -
75C GLN* 3.6 30.7 - - + +
78C ILE* 6.5 0.4 - - + -
109C ILE* 4.1 5.6 - - + -
110C LEU 3.3 7.2 - - - +
111C SER* 4.0 9.9 - - - +
112C VAL* 5.7 0.9 - - + +
113C LEU* 4.9 0.2 - - + -
189C LEU* 5.1 4.3 - - + -
190C VAL* 1.3 78.5 - - - +
192C THR* 1.3 63.4 + - - +
193C PHE* 3.5 31.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 192 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C PHE* 3.6 29.9 - - + -
33C THR* 4.1 15.7 - - + -
34C GLU 3.3 7.2 - - - +
35C GLN* 2.9 24.6 + - - +
109C ILE* 3.8 3.3 - - - +
110C LEU* 2.9 52.7 + - + -
173C LEU 4.8 2.8 + - - -
190C VAL* 4.1 5.7 - - - +
191C ILE* 1.3 75.5 - - - +
193C PHE* 1.3 66.7 + - - +
194C PRO* 3.4 10.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 193 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C GLU* 2.7 63.2 + - + +
36C LEU* 4.7 4.0 - - + -
75C GLN* 4.2 13.2 - - + -
78C ILE* 3.4 49.6 - - + -
79C GLU* 4.5 4.7 - - + -
92C LEU* 3.8 24.0 - - + -
108C THR 4.3 1.8 - - - +
109C ILE* 3.3 34.8 - - + -
191C ILE* 3.5 30.1 - - + -
192C THR* 1.3 73.5 - - - +
194C PRO* 1.3 68.2 - - - +
195C VAL* 3.5 4.8 + - + -
211C TRP* 5.5 1.6 - + + -
215C PHE* 4.5 5.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 194 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C PHE* 3.6 37.0 - - + -
31C PHE* 4.9 2.9 - - + -
32C ARG 3.4 8.1 - - - +
33C THR* 4.4 3.4 - - + -
96C CYS* 3.8 6.6 - - - +
97C LEU* 3.3 38.3 + - + +
108C THR* 3.1 38.6 - - + +
110C LEU* 5.1 1.1 - - + -
192C THR* 3.4 11.0 - - + +
193C PHE* 1.3 85.0 - - - +
195C VAL* 1.3 62.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 195 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C PHE* 3.3 6.0 - - - -
32C ARG* 2.7 48.6 + - + +
34C GLU* 3.7 36.1 - - + +
92C LEU* 4.3 20.4 - - + -
95C ILE* 3.4 37.0 - - + +
96C CYS* 4.5 0.2 - - - +
193C PHE* 3.9 1.8 - - + +
194C PRO* 1.3 78.4 - - - +
196C ASN* 1.3 72.6 + - - +
208C ALA* 4.5 6.7 - - + -
211C TRP* 4.9 2.0 - - + -
212C GLU* 5.4 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 196 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C PHE 3.9 2.0 - - - +
31C PHE* 3.1 30.2 - - - -
32C ARG* 5.1 0.9 - - - +
95C ILE 3.0 24.2 + - - +
96C CYS 3.3 19.6 + - - -
97C LEU* 4.1 1.2 - - - +
195C VAL* 1.3 79.7 - - - +
197C ASN* 1.3 64.1 + - - +
198C TYR* 3.4 50.0 + - + +
205C LEU* 5.6 0.3 - - - +
208C ALA* 4.5 3.1 - - - +
----------------------------------------------------------
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