Contacts of the strand formed by residues 250 - 256 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A ILE 3.8 0.9 - - - +
163A ILE* 2.9 41.7 + - + +
239A PRO 5.9 0.2 - - - +
240A TYR* 3.1 24.4 - - + -
241A GLU* 3.0 37.7 - - + +
243A PRO* 2.9 38.3 - - - +
244A GLN 5.2 0.2 - - - +
249A PHE* 1.3 69.8 - - - +
251A THR* 1.3 60.2 + - - +
252A ILE* 3.9 13.5 + - + +
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Residues in contact with THR 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A GLN* 5.6 0.2 + - - -
160A PRO* 5.0 2.8 - - - +
161A ILE 3.5 8.9 + - - -
162A GLN* 3.8 22.9 + - - +
241A GLU* 4.4 13.2 + - - +
244A GLN* 6.2 3.8 - - + -
247A THR* 5.8 2.9 - - + -
249A PHE 4.4 7.6 - - - +
250A THR* 1.3 73.9 - - - +
252A ILE* 1.3 62.5 + - - +
253A LEU* 3.8 25.5 - - - +
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Residues in contact with ILE 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A ILE* 3.1 36.5 + - + +
163A ILE* 3.6 29.2 - - + -
175A ILE* 3.7 12.3 - - + -
217A VAL* 4.1 11.9 - - + -
220A ASN* 6.1 1.3 - - + +
238A VAL* 4.0 25.8 - - + -
239A PRO 6.0 0.4 - - - +
241A GLU* 6.4 0.9 - - + -
250A THR* 4.5 14.4 - - + +
251A THR* 1.3 77.7 - - - +
253A LEU* 1.3 66.8 + - - +
254A TYR* 3.5 44.9 + - + +
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Residues in contact with LEU 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A THR* 4.1 21.3 - - + -
159A CYS 3.7 4.7 - - - +
160A PRO* 4.1 17.7 - - + -
217A VAL* 3.0 25.7 - - + +
218A GLU* 3.1 41.6 + - + +
219A GLY* 5.6 0.7 - - - -
220A ASN* 5.6 2.0 - - + +
251A THR* 3.8 21.5 - - - +
252A ILE* 1.3 84.7 - - - +
254A TYR* 1.3 61.6 + - - +
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Residues in contact with TYR 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A THR* 4.8 0.5 - - - -
159A CYS* 3.2 35.9 + - - +
161A ILE* 3.3 38.4 - - + -
163A ILE* 6.4 0.2 - - + -
175A ILE* 3.2 33.0 + - - +
177A ALA* 3.3 32.1 - - + +
215A ILE* 4.2 3.8 - - + -
216A ARG 3.3 4.5 - - - +
217A VAL* 4.1 17.0 - - + -
218A GLU* 5.9 0.2 - - - -
236A VAL 5.3 2.0 - - - -
238A VAL* 5.2 1.3 - - + +
252A ILE* 3.5 28.6 - - + +
253A LEU* 1.3 79.5 - - - +
255A ASN* 1.3 61.6 + - - +
256A PHE* 3.7 22.9 - + + -
273A ILE* 6.1 0.2 - - + -
275A ILE* 3.7 21.9 - - + +
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Residues in contact with ASN 255 (chain A).
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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156A ALA* 3.0 39.7 - - - +
157A LYS 3.3 13.1 + - - +
158A THR* 4.7 1.1 - - - -
214A LEU 3.2 1.3 - - - +
215A ILE* 3.2 7.3 - - - +
216A ARG* 2.6 55.4 + - + +
217A VAL* 4.6 2.9 - - - +
218A GLU* 3.9 24.0 - - + +
254A TYR* 1.3 74.5 - - - +
256A PHE* 1.3 76.1 + - - +
257A MET* 4.0 7.6 - - - -
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Residues in contact with PHE 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A LEU* 4.4 18.6 - - + -
153A CYS* 3.8 15.3 - - - -
154A GLN 3.9 1.9 + - - +
155A ILE* 3.5 5.5 - - - -
156A ALA 2.6 32.6 + - - -
157A LYS 4.8 0.8 + - - -
159A CYS* 4.2 13.7 - - + -
161A ILE* 5.5 1.3 - - + -
214A LEU* 3.5 11.4 - - + -
215A ILE* 4.0 23.1 - - + -
254A TYR* 3.7 37.7 - + + -
255A ASN* 1.3 81.3 - - - +
257A MET* 1.3 56.7 + - - +
258A CYS 4.0 0.4 - - - -
271A ILE* 5.4 0.9 - - + -
273A ILE* 4.0 38.6 - - + -
290A PHE* 5.4 1.8 - + - -
294A ILE* 3.1 32.8 - - + -
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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