Contacts of the strand formed by residues 188 - 197 (chain C) in PDB entry 6VSB
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 ASN 188 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95C THR* 3.3 33.1 - - - +
99C ASN 5.9 0.9 + - - -
176C LEU 5.9 1.2 + - - -
187C LYS* 1.3 86.1 + - - +
189C LEU* 1.3 73.9 + - - +
190C ARG* 4.3 8.7 - - - +
207C HIS* 4.8 12.3 - - - +
208C THR 3.3 13.9 - - - +
209C PRO* 3.7 7.6 - - + -
210C ILE* 4.1 7.5 - - - +
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Residues in contact with LEU 189 (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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34C ARG* 4.7 20.0 - - - +
91C TYR* 5.8 1.8 - - - +
93C ALA* 5.8 3.1 - - + -
94C SER 3.8 7.0 - - - +
95C THR* 4.2 10.3 - - + -
188C ASN* 1.3 80.1 - - - +
190C ARG* 1.3 62.6 + - - +
191C GLU* 2.9 47.7 - - + +
207C HIS* 4.0 0.9 - - - -
208C THR* 2.6 41.8 + - + +
209C PRO 3.6 9.6 - - - +
210C ILE* 3.5 24.9 - - + -
216C LEU* 5.6 9.4 - - + -
217C PRO* 3.5 23.6 - - + -
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Residues in contact with ARG 190 (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 PHE* 5.1 1.7 - - + -
93C ALA* 3.1 6.5 - - - +
94C SER* 3.0 43.3 + - - +
176C LEU 5.9 1.3 - - - +
188C ASN* 4.3 7.2 - - - +
189C LEU* 1.3 72.0 - - - +
191C GLU* 1.3 64.2 + - - +
192C PHE* 4.7 16.8 - - + -
206C LYS 4.0 9.0 - - - +
207C HIS* 4.5 13.7 - - + -
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Residues in contact with GLU 191 (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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34C ARG* 5.6 7.0 - - + -
91C TYR* 4.0 24.7 - - + +
92C PHE 3.2 7.9 - - - +
93C ALA* 4.2 0.9 - - + +
189C LEU* 2.9 35.2 - - + +
190C ARG* 1.3 74.8 - - - +
192C PHE* 1.3 75.2 + - - +
205C SER* 3.4 12.3 - - - -
206C LYS* 3.1 33.4 + - + +
208C THR* 3.5 14.0 + - - -
221C SER* 5.1 3.8 + - - -
223C LEU* 3.5 28.2 - - + +
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Residues in contact with PHE 192 (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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90C VAL 4.5 0.2 - - - -
91C TYR* 3.4 3.8 - - - -
92C PHE* 2.5 62.9 + + + +
104C TRP* 3.3 37.2 - + - -
175C PHE* 4.7 22.4 - + + -
176C LEU 6.1 0.4 - - - -
190C ARG* 4.7 14.8 - - + -
191C GLU* 1.3 94.7 - - - +
193C VAL* 1.3 64.2 + - - +
194C PHE* 3.5 33.0 - + + -
203C ILE* 5.7 1.6 - - + -
204C TYR 3.3 14.1 - - - -
205C SER* 3.3 24.2 - - - -
206C LYS 4.7 4.3 - - - -
207C HIS* 5.0 5.4 - - - -
223C LEU* 4.7 0.7 - - - -
226C LEU* 5.8 0.2 - - + -
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Residues in contact with VAL 193 (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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35C GLY* 4.8 5.2 - - - +
37C TYR* 4.5 23.1 - - + -
90C VAL 4.0 2.7 - - - -
91C TYR* 4.2 16.2 - - + -
192C PHE* 1.3 79.1 - - - +
194C PHE* 1.3 69.5 + - - +
195C LYS* 5.2 1.8 - - + +
204C TYR* 2.9 50.7 + - + -
223C LEU* 3.5 25.6 - - + -
270C LEU* 3.7 33.4 - - + -
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Residues in contact with PHE 194 (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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86C PHE* 3.4 17.8 - + + -
89C GLY* 3.1 26.2 - - - -
90C VAL* 3.3 21.3 + - + -
92C PHE* 5.2 6.5 - + + -
104C TRP* 4.6 21.1 - + - -
106C PHE* 3.3 41.5 - + - -
119C ILE* 6.5 0.4 - - + -
175C PHE* 6.6 0.2 - + - -
192C PHE* 3.5 41.1 - + + -
193C VAL* 1.3 88.9 - - - +
195C LYS* 1.3 61.0 + - - +
201C PHE* 4.6 7.6 - - + -
202C LYS 3.8 2.9 - - - -
203C ILE* 3.5 35.0 - - + -
238C PHE* 5.7 1.6 - + - -
270C LEU* 4.4 1.4 - - - +
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Residues in contact with LYS 195 (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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37C TYR* 5.6 4.3 - - + +
54C LEU* 4.8 11.2 - - + -
86C PHE* 4.5 2.5 - - - -
88C ASP 4.7 7.0 - - - +
89C GLY* 4.7 2.7 - - - -
193C VAL* 4.2 2.2 - - + -
194C PHE* 1.3 74.4 - - - +
196C ASN* 1.3 61.2 + - - +
197C ILE* 3.8 5.8 - - + +
200C TYR 3.4 2.1 - - - +
201C PHE* 3.4 7.8 - - - -
202C LYS* 3.1 39.8 + - + +
204C TYR* 5.0 12.3 - - + -
270C LEU* 4.8 9.9 - - + -
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Residues in contact with ASN 196 (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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54C LEU* 5.6 4.2 - - - +
86C PHE* 4.3 16.5 - - + -
88C ASP* 4.9 8.3 + - - +
195C LYS* 1.3 72.6 - - - +
197C ILE* 1.3 59.3 + - - +
198C ASP 4.1 1.4 + - - -
199C GLY* 4.8 6.1 - - - +
200C TYR 3.8 4.3 - - - +
201C PHE* 3.9 23.8 - - + +
233C ILE 5.4 6.7 - - - +
235C ILE* 5.2 6.1 - - + -
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Residues in contact with ILE 197 (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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54C LEU* 5.7 7.6 - - + -
195C LYS* 3.8 7.4 - - + -
196C ASN* 1.3 72.7 - - - +
198C ASP* 1.3 66.8 + - + +
199C GLY 3.1 0.7 - - - -
200C TYR* 2.9 37.9 + - - +
202C LYS* 5.4 10.8 - - + -
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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