Contacts of the helix formed by residues 340 - 347 (chain D) in PDB entry 1XVP
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 MET 340 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161D PHE* 4.9 0.2 - - + -
162D ALA* 3.8 11.4 - - + +
165D ASN* 3.5 35.4 - - - +
166D THR* 2.8 24.0 - - - +
326D TYR* 3.6 20.2 - - - +
330D ILE* 3.8 19.3 - - + -
336D LEU* 3.5 39.0 + - + +
337D SER* 3.2 10.9 - - - +
338D ALA 3.2 0.2 - - - -
339D MET* 1.3 78.5 - - - +
341D PRO* 1.3 66.1 - - - +
342D LEU 3.2 2.2 - - - -
343D LEU* 3.7 13.5 - - + -
344D GLN 3.2 14.4 + - - -
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Residues in contact with PRO 341 (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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166D THR* 5.3 2.9 - - + +
337D SER 4.2 0.9 - - - +
338D ALA* 3.8 8.5 - - - +
339D MET 3.5 9.0 - - - +
340D MET* 1.3 86.6 - - - +
342D LEU* 1.3 65.8 + - + +
344D GLN* 3.2 35.1 + - + +
345D GLU* 3.2 16.1 + - - +
689H ILE* 4.5 18.8 - - + -
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Residues in contact with LEU 342 (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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166D THR* 4.2 32.5 - - + +
169D VAL* 4.1 19.7 - - + -
170D LEU* 4.4 11.4 - - + -
173D ILE* 4.2 15.7 - - + -
340D MET 3.2 0.4 - - - -
341D PRO* 1.3 78.3 - - + +
343D LEU* 1.3 61.5 + - + +
344D GLN 3.0 1.3 - - - -
345D GLU* 2.8 26.4 + - - +
346D ILE* 3.1 16.3 + - + +
689H ILE* 3.5 35.2 - - + +
690H LEU* 3.8 21.3 - - + -
693H LEU* 5.4 2.0 - - + -
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Residues in contact with LEU 343 (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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165D ASN* 2.8 30.3 - - - +
166D THR* 3.5 29.8 - - - +
169D VAL* 3.6 29.8 - - + -
199D VAL* 4.2 9.2 - - + -
326D TYR* 3.9 17.7 - - + +
330D ILE* 4.8 4.7 - - + -
340D MET* 3.5 25.4 + - + +
341D PRO 3.5 0.4 - - - -
342D LEU* 1.3 82.3 - - + +
344D GLN* 1.3 56.8 + - - +
346D ILE* 3.0 9.8 + - + +
347D CYS* 2.9 34.0 + - - +
1003D CID 4.1 8.7 - - + -
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Residues in contact with GLN 344 (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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330D ILE* 4.7 11.6 - - - +
331D GLN* 5.8 1.6 - - - +
337D SER* 3.6 29.9 + - - +
338D ALA* 4.8 4.3 - - - -
340D MET 3.2 11.0 + - - +
341D PRO* 3.2 27.6 + - - +
343D LEU* 1.3 81.0 - - - +
345D GLU* 1.3 61.5 + - + +
347D CYS 3.6 9.2 - - - +
348D SER* 3.3 18.0 - - - -
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Residues in contact with GLU 345 (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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195D LYS* 3.8 8.7 + - - +
341D PRO 3.2 12.7 + - - +
342D LEU 2.8 10.1 + - - +
344D GLN* 1.3 85.6 + - - +
346D ILE* 1.3 59.3 + - - +
347D CYS 3.4 0.2 - - - -
348D SER* 2.6 26.5 + - - -
686H ARG* 5.8 0.5 - - - +
687H HIS* 3.7 31.0 + - + -
688H LYS* 3.9 1.9 + - - +
689H ILE* 3.1 49.1 + - - +
690H LEU* 3.4 21.9 + - + +
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Residues in contact with ILE 346 (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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169D VAL* 4.2 24.2 - - + -
173D ILE* 6.0 1.1 - - + -
194D LEU* 3.8 15.9 - - + +
195D LYS* 3.1 40.9 + - - +
198D ALA* 3.6 26.7 - - + -
199D VAL* 4.1 18.2 - - + +
323D ASN* 5.7 1.3 - - - +
342D LEU* 3.4 14.6 - - + +
343D LEU* 3.0 17.2 + - + +
345D GLU* 1.3 77.2 - - - +
347D CYS* 1.3 59.8 + - - +
348D SER* 3.1 4.9 + - - +
690H LEU* 3.9 29.8 - - + -
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Residues in contact with CYS 347 (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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199D VAL* 4.0 15.3 - - - -
323D ASN* 4.6 9.4 - - - -
326D TYR* 3.7 35.7 - - - -
327D GLY* 3.8 22.4 - - - -
330D ILE* 3.9 9.2 - - + -
331D GLN* 4.1 11.8 - - - +
343D LEU* 2.9 16.4 + - - +
344D GLN 3.6 7.6 - - - +
346D ILE* 1.3 77.2 - - - +
348D SER* 1.3 56.0 + - - +
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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