Contacts of the strand formed by residues 497 - 501 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276J GLN* 3.6 1.8 - - - -
184K LEU 3.9 1.0 - - - +
185K THR* 3.3 0.8 - - - -
186K LEU* 2.9 38.6 + - - +
188K VAL* 3.9 22.7 - - + -
324K LEU* 5.3 3.1 - - + +
327K LEU* 4.0 27.4 - - + +
328K PHE* 4.4 5.2 - - + +
331K ALA* 4.5 3.1 - - + -
473K VAL* 3.9 20.0 - - + -
475K THR* 2.6 37.5 - - + -
495K PRO* 3.2 25.5 + - + +
496K LEU* 1.3 75.7 - - - +
498K THR* 1.3 60.0 + - - +
499K PHE* 3.9 15.9 - - + -
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Residues in contact with THR 498 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276J GLN* 2.7 33.0 + - - +
277J GLU* 3.9 15.7 - - + +
183K SER* 4.1 11.4 - - - -
184K LEU 3.3 6.3 - - - +
185K THR* 2.8 22.6 + - - +
472K LEU 3.4 1.4 - - - +
473K VAL* 3.4 9.0 - - - +
474K GLU* 3.0 49.7 + - - +
497K LEU* 1.3 72.2 - - - +
499K PHE* 1.3 66.7 + - - +
500K ARG* 4.1 7.4 - - - +
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Residues in contact with PHE 499 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168K PHE* 5.8 2.5 - + - -
172K LEU* 3.9 24.9 - - + -
176K VAL* 3.5 11.8 - - + +
183K SER* 3.1 5.2 - - - -
184K LEU* 2.7 34.0 + - + +
186K LEU* 4.0 15.9 - - + -
188K VAL* 3.5 33.9 - - + -
327K LEU* 4.1 18.6 - - + -
467K VAL* 3.8 17.0 - - + -
471K PHE* 4.1 22.2 - - + -
472K LEU 3.5 2.2 - - - -
473K VAL* 3.6 28.5 - - + -
497K LEU* 3.9 16.8 - - + -
498K THR* 1.3 75.9 - - - +
500K ARG* 1.3 59.6 + - - +
501K ALA 4.1 0.2 - - - -
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Residues in contact with ARG 500 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276J GLN 4.6 0.2 + - - -
277J GLU* 3.1 34.8 + - - +
280J PHE* 3.7 8.3 - - - +
281J ASN* 3.6 36.0 + - - +
181K ARG* 4.0 15.5 + - - +
182K GLY 3.7 9.2 - - - +
183K SER* 3.8 19.0 + - - -
471K PHE* 3.2 4.7 - - - +
472K LEU* 2.8 55.2 + - + +
474K GLU* 3.0 36.0 + - - +
498K THR* 4.0 5.9 - - - +
499K PHE* 1.3 72.1 - - - +
501K ALA* 1.3 70.6 + - - +
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Residues in contact with ALA 501 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173K LYS* 4.7 6.7 - - + -
176K VAL* 3.7 16.2 - - + -
177K LEU* 4.1 18.2 - - + -
182K GLY* 3.0 19.8 + - - +
470K HIS 3.5 8.3 - - - +
471K PHE* 3.8 10.4 - - + -
472K LEU* 5.6 0.7 - - - +
499K PHE 4.1 0.4 + - - -
500K ARG* 1.3 83.5 - - - +
502K ILE* 1.3 73.4 + - - +
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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