Contacts of the strand formed by residues 109 - 121 (chain C) in PDB entry 1SMV
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 LYS 109 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B TYR* 3.9 26.2 + - + +
191B GLU 2.9 23.5 + - - -
192B LEU* 3.8 4.6 - - - +
193B GLY* 3.7 15.0 - - - +
221B PRO 4.9 3.0 + - - -
107C TRP* 4.3 3.4 - - - +
108C SER* 1.3 84.5 - - - +
110C TYR* 1.3 66.4 + - - +
196C TRP* 3.7 23.6 - - + +
197C TYR 3.2 17.9 - - - +
198C PRO* 4.3 7.2 - - + -
199C TYR* 4.3 1.6 - - - +
250C MET* 3.6 4.0 - - - +
251C ILE* 3.0 38.7 + - + +
252C GLU* 2.7 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 110 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C MET* 3.9 11.6 - - - +
93C PRO* 3.3 43.9 - - + +
104C ALA* 6.0 2.0 - - + -
109C LYS* 1.3 78.6 - - - +
111C SER* 1.3 69.4 + - - +
112C TRP* 3.8 22.4 - + - -
195C LYS 3.6 0.3 - - - +
196C TRP* 3.4 9.9 - - - -
197C TYR* 2.9 60.9 + + + +
198C PRO 3.3 24.4 + - - -
199C TYR* 4.1 9.9 - + + -
200C LYS 5.3 0.2 - - - -
219C LEU 4.0 5.2 + - - -
221C PRO* 4.0 10.7 - - - +
248C ILE* 3.9 18.2 - - + -
249C GLN 3.0 15.0 - - - +
250C MET* 4.5 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 111 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C TYR* 1.3 81.9 - - - +
112C TRP* 1.3 69.0 + - - +
113C LEU 3.5 0.3 + - - -
195C LYS* 2.9 54.0 + - - +
196C TRP* 3.6 15.9 - - - -
197C TYR* 5.7 0.2 - - - -
248C ILE* 3.6 2.1 - - - -
249C GLN* 2.9 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 112 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C VAL* 3.1 30.5 + - + +
92C MET 3.8 2.0 - - - -
93C PRO* 3.7 19.7 - - + -
96C VAL* 3.7 33.9 - - + -
100C LEU* 3.8 17.0 - - + -
110C TYR* 3.8 17.6 - + - -
111C SER* 1.3 77.6 + - - +
113C LEU* 1.3 64.7 + - - +
114C SER 4.4 0.4 - - - -
115C VAL* 3.4 25.4 - - + -
187C LEU* 4.4 5.4 - - + -
189C VAL* 3.7 25.0 - - + +
192C LEU* 4.6 7.4 - - + +
195C LYS* 4.8 1.2 + - - -
197C TYR* 5.7 2.6 - + - -
221C PRO* 3.8 17.6 - - + +
246C TYR* 3.9 22.7 - + + -
247C THR 4.2 4.7 - - - -
248C ILE* 4.0 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 113 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C THR* 4.7 5.6 - - + -
111C SER 3.5 1.2 + - - -
112C TRP* 1.3 78.0 - - - +
114C SER* 1.3 64.5 + - - +
189C VAL* 3.8 16.5 - - + +
195C LYS* 4.8 6.5 - - - +
247C THR* 2.8 36.4 + - + +
249C GLN* 3.5 46.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 114 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C TRP 3.4 0.6 - - - -
113C LEU* 1.3 82.1 - - - +
115C VAL* 1.3 71.0 + - - +
116C ARG* 4.8 3.1 + - - +
186C THR* 5.9 1.0 - - - +
187C LEU 5.9 0.4 - - - -
189C VAL* 4.5 5.8 - - - -
245C THR 4.5 4.3 + - - -
246C TYR* 3.2 5.0 - - - +
247C THR* 2.9 41.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 115 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C VAL* 4.2 11.2 - - + -
96C VAL* 5.4 2.2 - - + -
112C TRP* 3.4 46.0 - - + -
114C SER* 1.3 82.5 + - - +
116C ARG* 1.3 62.0 + - - +
117C TYR* 3.7 27.7 - - + +
186C THR* 3.3 5.6 - - - -
187C LEU* 3.0 47.3 + - + +
189C VAL* 4.9 0.2 - - - +
244C ASP* 3.7 12.8 - - - +
245C THR 3.7 3.4 - - - -
246C TYR* 4.4 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 116 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C SER* 5.2 3.4 - - - +
115C VAL* 1.3 75.1 - - - +
117C TYR* 1.3 66.6 + - - +
118C THR* 3.6 10.3 - - - +
170C PHE* 3.6 48.8 - - - -
184C SER* 2.9 43.0 + - - +
185C THR* 3.3 7.8 - - - +
186C THR* 3.5 25.6 - - + +
243C TYR 3.7 0.7 - - - +
244C ASP* 3.3 5.8 - - - +
245C THR* 2.9 46.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 117 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C THR* 4.0 12.8 - - + -
89C GLU* 3.0 26.0 + - - -
90C LEU 4.9 0.2 - - - -
91C VAL* 3.6 20.3 - - + +
96C VAL* 4.0 7.0 - - + +
115C VAL* 3.7 15.6 - - + +
116C ARG* 1.3 72.7 - - - +
118C THR* 1.3 62.3 + - - +
133C MET* 4.6 8.4 - - - +
135C PHE* 4.2 28.5 - + - -
183C ILE 4.3 0.2 - - - +
184C SER* 3.1 3.6 + - - -
185C THR* 2.9 39.7 + - + +
224C LEU* 3.6 38.0 - - + +
242C ILE* 4.0 20.9 - - + -
243C TYR 3.5 1.8 - - - -
244C ASP* 2.9 28.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 118 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C ARG* 3.6 13.7 - - - +
117C TYR* 1.3 73.7 - - - +
119C TYR* 1.3 68.0 + - - +
120C ILE* 3.9 1.5 + - + +
133C MET* 5.6 0.2 - - - -
167C GLY* 3.6 33.9 - - - +
170C PHE* 4.1 5.6 - - + +
171C ILE* 4.3 18.1 - - + +
183C ILE 3.6 3.8 - - - +
184C SER* 3.0 26.1 + - - +
242C ILE* 3.4 5.5 - - - +
243C TYR* 2.9 37.4 + - - +
245C THR* 4.5 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 119 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C ILE* 4.0 10.3 - - + -
118C THR* 1.3 73.1 - - - +
120C ILE* 1.3 60.8 + - - +
121C PRO* 3.9 7.2 - - + -
131C ILE* 3.5 31.2 - - + -
133C MET* 4.7 3.5 - - + +
160C GLN 4.4 1.3 - - - -
161C VAL* 2.6 40.7 + - + +
163C SER 3.5 21.1 - - - -
164C GLY* 3.4 20.6 - - - +
183C ILE* 2.8 41.1 + - + +
239C ALA* 3.2 26.2 + - - +
240C GLY* 3.8 20.9 - - - -
241C ARG 3.6 13.9 - - - -
242C ILE* 4.1 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 120 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C ALA* 4.0 18.8 - - + +
53C VAL* 4.5 4.5 - - + -
118C THR* 4.6 1.8 - - + +
119C TYR* 1.3 84.4 - - - +
121C PRO* 1.3 77.7 - - + +
164C GLY 4.0 12.3 - - - +
165C SER* 4.5 4.9 - - - -
167C GLY 4.5 1.8 - - - -
168C LEU* 4.1 22.2 - - + +
171C ILE* 3.7 30.7 - - + -
240C GLY* 3.5 0.2 - - - -
241C ARG* 3.0 54.1 + - - +
243C TYR* 4.0 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 121 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C GLN* 4.1 22.0 - - + +
51C ALA* 5.8 1.0 - - + +
119C TYR* 3.9 4.9 - - + -
120C ILE* 1.3 101.4 - - + +
122C SER* 1.3 60.3 + - - +
123C CYS 3.8 3.8 - - - +
161C VAL 3.7 15.9 - - - +
162C TRP* 3.7 15.9 - - - +
163C SER 3.3 31.6 - - - +
164C GLY 4.1 0.2 - - - -
165C SER* 3.9 15.5 - - - +
239C ALA 3.9 5.8 - - - +
241C ARG* 3.9 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