Contacts of the strand formed by residues 250 - 256 (chain I) 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 THR 250 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162I GLN* 3.5 1.9 - - - -
163I ILE* 2.8 46.7 + - + +
175I ILE* 5.8 0.2 - - + -
240I TYR* 3.6 18.1 + - + -
241I GLU* 2.7 42.4 + - + +
242I PRO 3.6 2.0 - - - +
243I PRO* 3.6 14.0 - - - +
249I PHE* 1.3 73.0 - - - +
251I THR* 1.3 67.5 + - - +
252I ILE* 4.1 12.4 + - + -
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Residues in contact with THR 251 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132I GLN* 5.8 1.3 + - - +
160I PRO* 3.9 24.2 - - + -
161I ILE 3.4 11.2 - - - +
162I GLN* 3.7 21.4 + - - +
247I THR* 5.7 1.4 - - - +
249I PHE* 3.6 9.4 + - - +
250I THR* 1.3 80.2 - - - +
252I ILE* 1.3 66.3 + - - +
253I LEU* 4.2 12.3 + - + +
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Residues in contact with ILE 252 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160I PRO* 3.4 3.3 - - - +
161I ILE* 2.9 34.0 + - + +
163I ILE* 3.2 32.3 - - + -
175I ILE* 3.8 25.6 - - + -
217I VAL* 3.6 18.8 - - + -
238I VAL* 3.8 20.2 - - + -
250I THR* 4.1 10.3 + - + -
251I THR* 1.3 78.7 - - - +
253I LEU* 1.3 64.2 + - - +
254I TYR* 3.5 33.4 + - + +
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Residues in contact with LEU 253 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158I THR* 4.2 18.6 - - + -
159I CYS 3.9 1.3 - - - -
160I PRO* 3.4 28.0 - - + -
217I VAL* 3.1 11.0 - - - +
218I GLU* 2.5 64.0 + - + +
219I GLY* 5.1 3.4 - - - -
251I THR* 4.2 11.9 - - + +
252I ILE* 1.3 77.0 - - - +
254I TYR* 1.3 55.5 + - - +
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Residues in contact with TYR 254 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158I THR* 3.9 0.5 - - - -
159I CYS* 2.7 42.6 + - - +
161I ILE* 3.7 43.1 - - + -
175I ILE* 4.1 14.2 + - - +
177I ALA* 3.3 34.5 + - + +
215I ILE* 3.7 13.0 - - + -
216I ARG 3.6 13.9 - - - +
217I VAL* 3.8 17.9 - - + -
236I VAL* 4.4 4.2 + - + -
238I VAL* 5.2 1.5 - - + +
252I ILE* 3.5 33.7 - - + +
253I LEU* 1.3 74.3 - - - +
255I ASN* 1.3 67.4 + - - +
256I PHE* 4.0 22.7 - + + -
273I ILE* 6.4 2.0 - - + -
275I ILE* 4.5 5.5 - - + +
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Residues in contact with ASN 255 (chain I).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156I ALA* 3.1 15.9 + - - +
157I LYS 2.9 23.3 + - - -
214I LEU 3.8 0.7 - - - +
215I ILE* 3.8 3.1 - - - +
216I ARG* 2.9 45.2 + - + +
218I GLU* 3.2 42.0 + - + +
254I TYR* 1.3 79.3 + - - +
256I PHE* 1.3 64.0 + - - +
257I MET* 4.2 13.7 - - - +
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Residues in contact with PHE 256 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151I LEU* 4.1 26.2 - - + -
153I CYS* 3.6 21.8 - - - -
155I ILE* 3.3 7.3 - - - +
156I ALA* 2.5 33.2 + - - +
157I LYS 4.5 2.0 + - - -
159I CYS* 4.1 9.4 - - + -
161I ILE* 6.2 1.3 - - + -
214I LEU* 3.9 7.6 - - + -
215I ILE* 3.7 31.4 - - + -
254I TYR* 4.0 26.5 - + + -
255I ASN* 1.3 73.7 - - - +
257I MET* 1.3 59.0 + - - +
258I CYS 3.5 1.3 - - - -
271I ILE* 6.0 0.2 - - + -
273I ILE* 3.8 34.3 - - + -
290I PHE* 6.1 0.4 - + - -
294I ILE* 3.2 36.3 - - + -
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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