Contacts of the strand formed by residues 497 - 501 (chain D) in PDB entry 4DVQ
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 LEU 497 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B GLN* 3.9 0.4 - - - -
185D THR* 3.5 1.3 - - - -
186D LEU* 2.9 40.0 + - - +
188D VAL* 3.8 25.6 - - + -
324D LEU* 5.2 2.0 - - + +
327D LEU* 4.0 26.0 - - + -
328D PHE* 4.6 7.0 - - + +
331D ALA* 3.9 15.3 - - + -
473D VAL* 4.5 8.7 - - + -
474D GLU 3.6 1.3 - - - +
475D THR* 3.2 27.1 - - + +
495D PRO* 3.8 24.0 - - + +
496D LEU* 1.3 76.6 - - - +
498D THR* 1.3 62.0 + - - +
499D PHE* 4.0 15.3 - - + -
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Residues in contact with THR 498 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B GLN* 3.0 24.9 + - - +
277B GLU* 3.9 14.3 - - + +
280B PHE* 6.1 0.2 - - - -
183D SER* 4.0 16.6 - - - -
184D LEU 3.5 3.4 - - - -
185D THR* 2.6 25.4 + - - +
472D LEU 3.4 1.2 - - - +
473D VAL* 3.3 7.3 - - - +
474D GLU* 2.8 57.0 + - - +
497D LEU* 1.3 71.8 - - - +
499D PHE* 1.3 67.3 + - - +
500D ARG* 4.3 3.8 - - - +
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Residues in contact with PHE 499 (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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168D PHE* 5.9 2.2 - + - -
172D LEU* 4.1 20.9 - - + -
176D VAL* 4.0 11.6 - - + +
183D SER* 3.1 5.0 - - - -
184D LEU 2.9 31.7 + - - +
186D LEU* 3.7 19.7 - - + -
188D VAL* 3.3 35.4 - - + -
327D LEU* 4.2 14.8 - - + -
467D VAL* 4.0 21.3 - - + -
471D PHE* 4.1 22.4 - - + -
472D LEU 3.4 2.2 - - - -
473D VAL* 4.0 28.9 - - + -
497D LEU* 3.9 16.4 - - + -
498D THR* 1.3 75.4 - - - +
500D ARG* 1.3 61.5 + - - +
501D ALA 4.1 0.2 - - - -
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Residues in contact with ARG 500 (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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277B GLU* 3.1 35.8 + - - +
280B PHE* 3.7 10.1 - - - +
281B ASN* 3.7 33.5 + - - +
181D ARG* 4.0 14.8 + - - +
182D GLY 3.9 8.5 - - - +
183D SER* 3.6 20.6 + - - -
471D PHE* 3.2 2.8 - - - +
472D LEU* 2.8 60.2 + - + +
474D GLU* 2.8 34.5 + - - +
498D THR* 3.9 3.4 - - - +
499D PHE* 1.3 72.5 - - - +
501D ALA* 1.3 72.3 + - - +
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Residues in contact with ALA 501 (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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173D LYS* 5.0 9.9 - - + -
176D VAL* 3.9 14.7 - - + +
177D LEU* 4.3 19.1 - - + -
182D GLY* 3.1 17.9 + - - +
470D HIS 3.3 11.7 - - - +
471D PHE* 3.9 9.8 - - + -
472D LEU* 5.7 1.3 - - - +
500D ARG* 1.3 78.7 - - - +
502D ILE* 1.3 66.5 + - - +
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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