Contacts of the strand formed by residues 150 - 154 (chain K) 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 LYS 150 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144K TYR* 3.3 4.3 - - - -
145K SER* 3.1 27.8 + - - -
148K LEU* 3.1 20.3 - - + +
149K LYS* 1.3 78.9 - - - +
151K LEU* 1.3 63.7 + - - +
152K TYR* 2.9 49.8 - - + +
270K PRO* 5.4 5.7 - - - +
291K GLU* 2.6 45.0 + - + +
292K GLY 5.4 0.2 + - - -
293K ARG* 4.2 20.5 - - + +
305K ASP* 3.6 20.0 + - - -
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Residues in contact with LEU 151 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131K PHE* 3.6 18.6 - - + -
142K TRP* 3.9 25.4 - - + -
143K THR 3.5 11.7 - - - +
144K TYR* 3.7 10.2 - - + -
149K LYS 4.3 0.2 + - - -
150K LYS* 1.3 73.1 - - - +
152K TYR* 1.3 77.0 + - - +
153K CYS* 3.9 5.6 + - + +
159K CYS* 4.9 6.7 - - + -
161K ILE* 4.7 3.8 - - + -
256K PHE* 4.3 22.4 - - + -
273K ILE* 5.8 0.4 - - + -
290K PHE* 3.3 39.7 - - + -
291K GLU 2.8 11.3 + - - +
292K GLY* 3.8 2.5 - - - -
293K ARG* 3.3 25.3 + - - +
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Residues in contact with TYR 152 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142K TRP* 2.8 25.8 - - - +
143K THR* 2.8 23.4 + - + -
145K SER* 4.4 3.5 - - - -
148K LEU* 4.7 2.1 - - - +
150K LYS* 2.9 60.2 - - + +
151K LEU* 1.3 76.2 - - - +
153K CYS* 1.3 59.7 + - - +
293K ARG* 3.7 29.4 - - + +
295K CYS* 4.4 2.2 - - - -
298K PRO* 3.5 33.5 - - + +
301K ASP* 3.1 22.2 - - + -
302K ARG* 3.3 34.0 + - + -
305K ASP* 3.4 19.8 - - - +
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Residues in contact with CYS 153 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141K THR 3.7 4.9 - - - -
142K TRP* 3.9 1.1 - - + -
151K LEU* 4.4 10.8 - - + -
152K TYR* 1.3 76.2 - - - +
154K GLN* 1.3 62.9 + - - +
159K CYS* 2.7 29.8 - - - -
256K PHE* 2.9 37.7 - - - -
292K GLY* 5.8 1.3 - - - -
293K ARG 3.3 6.7 + - - +
294K ILE* 3.4 22.3 - - - -
295K CYS 3.1 25.5 + - - +
298K PRO* 3.9 6.0 - - - +
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Residues in contact with GLN 154 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139K SER* 3.6 11.9 + - - +
140K ALA 3.1 23.6 + - - -
141K THR* 3.0 19.6 + - - +
153K CYS* 1.3 80.6 - - - +
155K ILE* 1.3 77.5 + - + +
156K ALA 3.6 0.6 + - - -
157K LYS* 3.8 38.6 + - + +
159K CYS* 4.7 0.5 - - - -
256K PHE* 4.1 2.6 + - - +
294K ILE* 3.6 7.0 - - - +
295K CYS 3.7 10.3 - - - +
296K ALA* 3.6 12.1 + - - +
298K PRO* 3.3 17.8 - - - +
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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