Contacts of the strand formed by residues 159 - 164 (chain D) in PDB entry 3VD1
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 CYS 159 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D THR 5.2 0.2 - - - -
142D TRP* 4.2 11.4 - - + -
151D LEU* 4.9 13.0 - - + -
153D CYS* 3.2 44.4 - - - -
157D LYS 3.5 13.7 - - - -
158D THR* 1.3 74.4 - - - +
160D PRO* 1.3 68.0 - - + +
161D ILE* 3.7 3.1 + - + +
252D ILE 3.6 1.6 - - - +
253D LEU* 4.5 1.6 - - - -
254D TYR* 3.0 36.5 + - + +
256D PHE* 4.1 17.5 - - + -
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Residues in contact with PRO 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A ALA* 4.6 12.6 - - + -
130D THR 4.9 0.3 - - - +
131D PHE* 4.2 11.6 - - - -
132D GLN* 3.6 35.2 + - - +
142D TRP* 3.0 38.7 - - + +
158D THR 3.5 5.6 - - - +
159D CYS* 1.3 79.0 - - - +
161D ILE* 1.3 64.7 + - - +
162D GLN 4.4 0.3 + - - -
251D THR* 5.6 6.7 - - + -
252D ILE 3.7 5.8 - - - +
253D LEU* 3.7 19.5 - - + -
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Residues in contact with ILE 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D VAL* 4.0 10.8 - - + -
130D THR 3.8 1.8 - - - -
131D PHE* 3.5 24.0 - - + -
151D LEU* 4.3 7.2 - - + -
159D CYS* 4.8 3.4 - - + +
160D PRO* 1.3 77.0 - - - +
162D GLN* 1.3 65.1 + - - +
163D ILE* 3.7 27.8 + - + -
250D THR 3.7 0.5 - - - +
251D THR* 3.3 6.7 - - - -
252D ILE* 3.0 35.5 + - + +
254D TYR* 4.0 30.7 - - + -
256D PHE* 5.7 2.5 - - + -
273D ILE* 6.0 0.2 - - + -
275D ILE* 4.9 4.0 - - + -
290D PHE* 3.4 34.3 - - + -
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Residues in contact with GLN 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D GLU 3.3 3.1 - - - +
129D VAL* 3.6 1.4 - - - -
130D THR* 2.6 69.5 + - - +
131D PHE* 3.7 9.4 - - - +
132D GLN* 4.0 38.2 - - - +
161D ILE* 1.3 75.6 - - - +
163D ILE* 1.3 61.2 + - - +
249D PHE* 3.6 37.6 - - + +
250D THR 3.7 3.1 - - - -
251D THR* 4.3 13.8 - - + +
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Residues in contact with ILE 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D PHE* 3.3 35.0 - - + -
128D GLU 3.7 0.2 - - - -
129D VAL* 3.9 24.9 - - + -
161D ILE* 3.8 22.0 - - + -
162D GLN* 1.3 75.5 - - - +
164D LYS* 1.3 63.0 - - - +
165D VAL* 5.8 0.2 - - + -
175D ILE* 4.6 12.3 - - + -
240D TYR* 5.0 7.6 - - + -
249D PHE* 3.6 2.0 - - - -
250D THR* 2.5 66.5 + - - +
252D ILE* 3.8 22.4 - - + -
254D TYR* 6.1 0.4 - - + +
275D ILE* 4.3 9.2 - - + -
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Residues in contact with LYS 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D HIS 3.4 1.5 - - - +
127D PHE* 3.5 8.5 - - - -
128D GLU* 3.0 56.6 + - + +
163D ILE* 1.3 77.8 - - - +
165D VAL* 1.3 77.4 + - - +
166D SER* 6.4 0.2 - - - +
248D GLU* 3.8 37.7 - - + +
249D PHE* 3.7 31.4 - - + -
250D THR* 4.5 0.4 - - - -
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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