Contacts of the strand formed by residues 497 - 501 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276I GLN* 3.7 2.7 - - - +
184L LEU 3.8 0.9 - - - +
185L THR* 3.3 1.0 - - - -
186L LEU* 2.8 40.3 + - - +
188L VAL* 3.7 27.4 - - + -
324L LEU* 5.2 3.6 - - + +
327L LEU* 3.9 33.9 - - + +
328L PHE* 4.4 5.4 - - + +
331L ALA* 3.9 13.5 - - + -
473L VAL* 4.1 9.9 - - + -
474L GLU 3.9 1.6 - - - +
475L THR* 3.2 32.1 - - + +
495L PRO* 3.3 22.9 + - + +
496L LEU* 1.3 73.9 - - - +
498L THR* 1.3 59.0 + - - +
499L PHE* 4.0 5.8 - - + -
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Residues in contact with THR 498 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276I GLN* 2.7 32.0 + - - +
277I GLU* 4.0 14.8 - - + +
280I PHE* 6.3 0.2 - - - -
183L SER* 4.0 16.2 - - - -
184L LEU 3.4 4.9 - - - +
185L THR* 3.0 21.9 + - - +
472L LEU 3.4 1.4 - - - +
473L VAL* 3.3 9.9 - - - +
474L GLU* 3.0 49.2 + - - +
497L LEU* 1.3 72.3 - - - +
499L PHE* 1.3 65.7 - - - +
500L ARG* 4.6 4.5 - - + +
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Residues in contact with PHE 499 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168L PHE* 5.7 2.0 - + - -
172L LEU* 3.7 30.5 - - + -
176L VAL* 3.9 7.7 - - + +
183L SER* 3.1 4.7 - - - -
184L LEU 2.7 40.2 + - - +
186L LEU* 3.9 17.3 - - + -
188L VAL* 3.4 46.0 - - + -
327L LEU* 4.2 17.5 - - + -
467L VAL* 4.0 20.9 - - + -
471L PHE* 4.3 13.0 - - + -
472L LEU 3.5 2.7 - - - -
473L VAL* 3.9 28.5 - - + -
497L LEU* 4.0 10.1 - - + -
498L THR* 1.3 74.8 - - - +
500L ARG* 1.3 59.4 + - - +
501L ALA 4.3 0.2 - - - -
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Residues in contact with ARG 500 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277I GLU* 3.2 38.2 + - - +
280I PHE* 4.2 0.6 + - - +
281I ASN* 3.6 36.4 + - - +
181L ARG* 3.7 22.6 + - - +
182L GLY 3.6 8.1 - - - +
183L SER* 3.7 9.3 + - - -
471L PHE* 3.1 6.7 - - - +
472L LEU* 2.9 60.1 + - + +
474L GLU* 3.0 29.6 + - - +
498L THR* 4.7 3.9 - - + +
499L PHE* 1.3 73.4 - - - +
501L ALA* 1.3 77.0 + - - +
502L ILE* 3.3 1.4 + - - +
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Residues in contact with ALA 501 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173L LYS* 5.0 8.7 - - - -
176L VAL* 4.0 14.0 - - + +
177L LEU* 4.1 19.3 - - + -
182L GLY* 3.0 18.5 + - - +
470L HIS 3.6 9.4 - - - +
471L PHE* 3.9 8.6 - - + -
472L LEU* 5.7 0.2 - - - +
500L ARG* 1.3 81.9 - - - +
502L ILE* 1.3 63.5 + - - +
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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