Contacts of the strand formed by residues 109 - 121 (chain C) in PDB entry 4SBV
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).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137B TYR* 3.8 28.3 + - + +
191B GLU 3.1 25.1 + - - -
192B VAL* 4.3 0.8 - - - +
193B SER* 3.4 30.4 + - - +
221B PRO 4.2 7.1 + - - -
107C TRP* 3.6 3.1 + - - -
108C SER* 1.3 91.1 - - - +
110C TYR* 1.3 57.5 + - - +
196C ARG* 4.3 13.0 - - + -
197C TYR 3.0 17.7 - - - +
198C PRO* 3.8 13.0 - - + -
199C PHE 4.4 0.9 - - - +
250C LEU* 5.2 0.4 - - - -
251C ILE* 3.1 34.3 + - + +
252C GLU* 3.0 30.3 + - - +
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Residues in contact with TYR 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C MET* 4.3 5.4 - - - +
93C PRO* 3.4 41.1 - - + +
104C ALA* 6.5 0.2 - - + -
109C LYS* 1.3 74.7 - - - +
111C ALA* 1.3 76.1 - - - +
112C TRP* 4.1 20.4 - + - -
196C ARG* 3.4 9.0 - - - +
197C TYR* 3.2 57.0 + + + +
198C PRO 3.4 25.5 + - - -
199C PHE* 4.1 9.0 - + + -
200C LYS 5.6 0.5 + - - -
219C LEU 3.7 11.8 + - - -
221C PRO* 4.6 2.9 - - + +
248C ILE* 3.9 21.3 - - + -
249C ARG* 3.1 16.6 - - - +
250C LEU* 4.0 8.1 - - + -
251C ILE* 5.2 0.9 - - - -
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Residues in contact with ALA 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C TYR* 1.3 86.5 - - - +
112C TRP* 1.3 67.8 + - - +
113C VAL* 4.0 0.9 - - + +
195C LYS 4.1 18.4 - - - +
196C ARG* 4.2 13.0 - - - +
197C TYR* 5.8 2.7 - - - -
248C ILE* 3.5 1.8 - - - -
249C ARG* 2.7 47.1 + - + +
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Residues in contact with TRP 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C VAL* 2.9 32.8 + - + +
93C PRO* 3.8 14.4 - - + -
96C VAL* 3.8 21.1 - - + -
100C LEU* 4.0 15.3 - - + -
110C TYR* 4.1 16.7 - + - -
111C ALA* 1.3 79.3 - - - +
113C VAL* 1.3 60.0 + - - +
114C ALA 4.1 10.3 - - - +
115C ILE* 3.6 25.6 - - + -
187C LEU* 4.4 11.2 - - + -
189C THR* 3.5 18.9 + - - +
192C VAL* 5.9 1.6 - - + -
197C TYR* 6.2 1.1 - + - -
221C PRO* 4.0 20.4 - - + +
246C TYR* 3.5 32.1 - + + -
247C THR 4.0 0.4 - - - -
248C ILE* 4.0 24.0 - - + -
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Residues in contact with VAL 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C ILE* 4.9 6.7 - - + -
111C ALA* 4.0 1.6 - - + +
112C TRP* 1.3 77.5 - - - +
114C ALA* 1.3 63.3 + - + +
189C THR* 3.8 20.7 + - - +
247C THR* 2.6 37.8 + - + +
248C ILE 4.1 0.9 - - - -
249C ARG* 4.0 26.0 - - + +
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Residues in contact with ALA 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C TRP* 3.6 2.0 - - - -
113C VAL* 1.3 85.8 - - + +
115C ILE* 1.3 60.7 + - - +
189C THR* 4.1 5.6 + - - -
245C SER 4.0 2.2 - - - +
246C TYR* 2.8 12.4 - - - +
247C THR* 2.8 47.4 + - - +
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Residues in contact with ILE 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C VAL* 3.9 14.4 - - + -
96C VAL* 4.0 21.1 - - + -
112C TRP* 3.6 46.9 - - + -
114C ALA* 1.3 76.8 - - - +
116C ARG* 1.3 64.2 + - - +
117C TYR* 3.8 25.0 - - + +
186C ALA* 3.2 6.1 - - - +
187C LEU* 2.9 72.9 + - + +
244C ALA* 4.9 3.1 - - + -
245C SER 3.1 4.9 + - - +
246C TYR* 4.2 5.6 - - + -
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Residues in contact with ARG 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C ILE* 1.3 76.7 - - - +
117C TYR* 1.3 63.7 + - - +
118C THR* 4.0 1.6 - - + -
170C PHE* 2.8 53.6 - - - -
184C THR* 3.0 34.8 - - - +
185C ILE 3.3 13.2 - - - +
186C ALA* 3.8 18.7 - - + +
243C TYR 3.1 0.7 - - - +
244C ALA* 3.1 8.1 - - - +
245C SER* 2.6 51.9 + - - +
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Residues in contact with TYR 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C SER* 4.3 15.0 - - - -
89C GLU* 4.8 8.2 - - + +
90C LEU 4.7 1.4 + - - -
91C VAL* 3.6 30.0 - - + +
96C VAL* 3.8 24.0 - - + +
115C ILE* 3.8 22.2 - - + +
116C ARG* 1.3 74.6 - - - +
118C THR* 1.3 63.1 + - - +
133C MET* 5.0 0.2 - - - -
135C PHE* 4.5 13.9 - + - -
183C ILE 3.9 0.9 - - - +
184C THR* 3.2 4.2 + - - -
185C ILE* 2.7 49.5 + - + +
224C LEU* 3.4 38.6 - - + -
242C LEU* 4.3 20.4 - - + -
243C TYR 3.3 5.8 - - - -
244C ALA* 4.0 21.5 - - + -
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Residues in contact with THR 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C ARG* 4.0 5.6 - - + -
117C TYR* 1.3 76.4 - - - +
119C TYR* 1.3 61.3 + - - +
120C LEU* 5.0 0.3 - - - +
167C GLY* 4.1 20.1 + - - -
170C PHE* 3.9 12.8 - - + -
171C VAL* 3.7 25.8 - - + +
183C ILE 3.6 5.4 + - - -
184C THR* 2.9 23.5 + - - +
242C LEU* 3.2 4.5 - - - +
243C TYR* 2.7 42.4 + - - +
245C SER* 3.8 17.3 - - - +
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Residues in contact with TYR 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C LEU* 4.8 8.3 - - + -
118C THR* 1.3 73.9 + - - +
120C LEU* 1.3 84.7 + - - +
121C PRO* 3.4 1.3 - - + +
131C ILE* 3.7 29.2 - - + -
133C MET* 4.4 5.8 - - + -
161C VAL* 2.9 11.3 + - - -
163C GLU 3.1 28.5 - - - -
164C GLY* 3.3 14.5 - - - +
167C GLY* 5.3 0.2 - - - -
183C ILE* 3.3 40.9 + - + +
228C MET* 5.1 0.7 - - + -
239C THR* 2.3 41.1 - - + +
240C GLY* 3.1 22.7 + - - -
241C ARG 3.5 10.8 - - - -
242C LEU* 3.8 8.1 - - + -
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Residues in contact with LEU 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C THR* 4.4 13.7 - - + +
53C VAL* 4.0 20.0 - - + -
118C THR* 5.2 0.2 - - - +
119C TYR* 1.3 91.1 - - - +
121C PRO* 1.3 71.8 - - + +
164C GLY 3.4 18.4 - - - +
165C GLN* 4.2 6.1 - - - -
167C GLY 4.4 2.0 - - - -
168C LEU* 3.7 30.3 - - + +
171C VAL* 4.2 13.9 - - + -
240C GLY* 2.9 21.8 - - - -
241C ARG* 2.9 25.9 + - - +
243C TYR* 3.8 30.5 - - + -
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Residues in contact with PRO 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C GLN* 3.5 30.1 - - + +
51C THR* 4.4 11.4 + - - +
119C TYR* 3.4 8.5 - - + +
120C LEU* 1.3 93.2 - - + +
122C SER* 1.3 62.5 + - - +
123C CYS 4.7 2.9 - - - +
161C VAL 3.7 5.4 - - - +
162C TRP* 3.1 33.9 - - - +
163C GLU 3.3 19.7 - - - +
164C GLY* 3.8 11.9 - - - -
165C GLN* 3.9 3.1 - - + +
239C THR 4.2 0.2 - - - +
241C ARG* 4.2 4.7 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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