Contacts of the strand formed by residues 159 - 164 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131J PHE* 5.2 0.2 - - - -
142J TRP* 4.1 18.6 - - - -
151J LEU* 3.7 27.8 - - - -
153J CYS* 3.4 31.4 - - - -
157J LYS 4.4 0.2 - - - +
158J THR* 1.3 77.7 - - - +
160J PRO* 1.3 61.9 - - - +
161J ILE* 3.6 12.5 + - - +
252J ILE 3.7 2.1 - - - +
253J LEU* 4.6 0.2 - - - -
254J TYR* 3.1 37.0 + - + +
256J PHE* 4.1 12.1 - - + -
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Residues in contact with PRO 160 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131J PHE* 4.1 12.0 - - - -
132J GLN* 3.9 36.0 + - + +
142J TRP* 3.3 39.0 - - + +
158J THR* 3.7 9.0 - - + +
159J CYS* 1.3 84.0 - - - +
161J ILE* 1.3 62.5 + - - +
162J GLN 4.1 0.4 - - - -
251J THR* 4.8 5.4 - - + -
252J ILE 3.8 6.5 - - - +
253J LEU* 3.9 15.9 - - + -
184K ALA* 5.7 8.3 - - + -
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Residues in contact with ILE 161 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129J VAL* 4.5 5.8 - - + -
130J THR 4.0 4.3 - - - +
131J PHE* 3.3 35.2 - - + -
151J LEU* 5.0 0.9 - - + -
159J CYS* 4.0 15.5 - - - +
160J PRO* 1.3 75.9 - - - +
162J GLN* 1.3 62.1 + - - +
163J ILE* 3.4 19.0 + - + +
251J THR* 4.8 1.8 - - - +
252J ILE* 3.3 30.9 + - + +
254J TYR* 3.9 24.5 - - + -
256J PHE* 6.2 2.9 - - + -
275J ILE* 3.4 33.4 - - + -
290J PHE* 4.8 5.6 - - + -
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Residues in contact with GLN 162 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128J GLU 4.3 0.2 - - - -
129J VAL* 3.1 3.6 - - - +
130J THR* 2.6 47.6 + - - +
131J PHE 3.3 9.4 + - - +
132J GLN* 3.2 58.7 + - + +
133J GLN 4.8 0.2 + - - -
160J PRO 4.0 0.2 + - - -
161J ILE* 1.3 70.5 - - - +
163J ILE* 1.3 55.1 + - - +
164J LYS 4.0 0.7 - - - -
249J PHE* 3.1 52.9 - - + -
251J THR* 4.1 9.6 + - - +
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Residues in contact with ILE 163 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127J PHE* 3.9 23.6 - - + -
128J GLU 3.7 4.0 - - - -
129J VAL* 4.1 18.6 - - + +
161J ILE* 3.4 28.9 + - + +
162J GLN* 1.3 79.5 - - - +
164J LYS* 1.3 62.3 + - - +
165J VAL* 5.0 2.3 - - + +
175J ILE* 3.3 35.0 - - + -
240J TYR* 5.6 2.5 - - + -
249J PHE* 3.7 7.7 - - - +
250J THR* 3.5 39.4 + - - +
252J ILE* 5.1 7.4 - - + -
275J ILE* 5.3 7.0 - - + -
277J LEU* 5.7 0.4 - - + -
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Residues in contact with LYS 164 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126J HIS* 3.8 29.1 + - - +
127J PHE* 3.7 3.5 - - - -
128J GLU* 3.0 57.3 + - + +
163J ILE* 1.3 73.7 - - - +
165J VAL* 1.3 85.8 - - - +
166J SER* 3.9 23.6 - - - +
248J GLU* 3.4 34.3 - - + +
249J PHE* 3.3 30.3 - - + +
250J THR* 5.8 0.9 - - - -
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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