Contacts of the strand formed by residues 167 - 172 (chain C) in PDB entry 3DVA
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 167 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C PHE 3.4 6.5 - - - +
99C LEU* 4.4 5.4 - - + -
151C ALA* 3.6 26.6 - - - +
154C VAL* 3.8 15.9 - - + -
155C ALA* 3.8 20.2 - - + +
158C LEU* 3.9 1.7 - - + +
166C VAL* 1.3 75.3 - - - +
168C ILE* 1.3 53.8 + - - +
194C PRO 3.0 6.3 + - - -
195C ALA* 3.2 3.6 - - + +
196C ILE* 2.7 33.3 + - - +
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Residues in contact with ILE 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C SER* 5.0 1.6 - - - +
92C LEU* 3.6 44.2 - - + -
96C ASP* 5.3 0.7 - - + -
97C PHE 2.9 15.2 + - - +
98C ILE* 3.4 12.6 - - + +
99C LEU* 2.9 26.6 + - - +
166C VAL* 4.0 3.6 - - + +
167C ALA* 1.3 75.6 - - - +
169C THR* 1.3 69.2 + - - +
170C TYR* 3.5 28.3 - - + +
196C ILE* 3.3 29.4 - - + +
198C VAL* 3.9 13.0 - - + -
245C VAL* 4.5 8.1 - - + -
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Residues in contact with THR 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C LEU* 2.7 23.8 + - - -
147C GLN* 2.9 21.8 - - - +
148C TYR* 3.7 14.4 - - + -
151C ALA* 3.7 23.6 - - + -
168C ILE* 1.3 75.2 - - - +
170C TYR* 1.3 69.8 + - - +
195C ALA* 6.5 0.2 - - + -
196C ILE 3.1 5.1 + - - +
197C PHE* 3.6 30.5 - - + -
198C VAL* 3.0 30.2 + - - +
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Residues in contact with TYR 170 (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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84C SER 4.2 3.8 - - - -
88C SER* 2.7 30.3 + - - -
89C HIS* 3.9 7.6 + - - +
92C LEU* 4.9 1.6 - - - +
98C ILE* 4.3 20.1 - - + +
99C LEU 3.5 2.8 + - - -
100C PRO* 4.8 2.7 - - + -
101C GLY* 4.0 5.0 + - - +
104C ASP* 3.1 27.0 - - + +
107C GLN* 3.5 39.5 - - + +
147C GLN* 3.0 21.4 + - - +
148C TYR* 4.2 2.5 - - - -
168C ILE* 3.5 29.9 - - + +
169C THR* 1.3 81.6 + - - +
171C THR* 1.3 61.1 + - - +
198C VAL* 3.4 38.1 - - + +
200C GLN* 3.6 12.1 - - - +
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Residues in contact with THR 171 (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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104C ASP* 5.3 0.7 - - - -
144C ILE* 4.0 8.5 - - - +
145C GLY* 4.8 2.1 + - - -
147C GLN* 3.7 13.2 + - - +
148C TYR* 3.3 37.2 - - + +
170C TYR* 1.3 75.4 - - - +
172C GLY* 1.3 65.3 + - - +
175C GLY* 3.7 20.4 - - - -
181C PHE* 4.2 10.3 - - + -
198C VAL 3.0 6.5 + - - -
199C VAL* 3.3 12.8 - - + -
200C GLN* 2.7 36.6 + - - +
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Residues in contact with GLY 172 (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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102C TYR* 6.2 0.2 - - - -
171C THR* 1.3 83.4 + - - +
173C ASP* 1.3 68.2 + - - +
174C GLY 3.3 2.7 - - - -
175C GLY 3.3 10.3 + - - +
176C THR* 3.7 13.7 + - - +
199C VAL* 4.0 3.5 - - - +
200C GLN* 3.2 14.4 - - - -
202C ASN* 6.3 0.7 - - - -
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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