Contacts of the strand formed by residues 458 - 466 (chain B) in PDB entry 3C0M
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 ASN 458 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221B GLY* 3.4 1.2 - - - -
222B ASP* 2.8 41.3 + - + +
223B THR* 5.0 1.8 - - - +
224B ALA 5.9 0.4 - - - +
277B LEU* 5.4 0.2 - - - +
453B SER* 4.0 23.8 - - - +
456B GLY* 4.2 8.8 + - - -
457B PHE* 1.3 77.9 + - - +
459B ASN* 1.3 69.8 + - - +
460B VAL* 2.7 20.3 + - - +
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Residues in contact with ASN 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B ARG* 3.1 13.2 - - - +
221B GLY* 3.2 4.0 - - - -
222B ASP* 2.7 27.9 - - - +
458B ASN* 1.3 78.2 - - - +
460B VAL* 1.3 62.5 + - - +
461B SER* 3.7 4.2 + - - -
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Residues in contact with VAL 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B LEU* 3.8 22.2 - - + -
220B ARG 3.0 6.3 - - - +
221B GLY* 3.8 3.8 - - - -
277B LEU* 5.9 3.1 - - + -
297B LEU* 6.6 0.2 - - + -
447B LEU* 4.5 15.4 - - + +
449B ALA* 5.6 4.9 - - - +
452B LEU* 3.6 37.0 - - + -
457B PHE* 3.6 28.7 - - + +
458B ASN 2.7 9.7 + - - +
459B ASN* 1.3 72.6 - - - +
461B SER* 1.3 66.1 + - - +
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Residues in contact with SER 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B THR 3.7 1.0 - - - +
219B LEU* 3.4 6.4 - - - +
220B ARG* 2.7 57.0 + - - +
447B LEU* 4.2 7.6 - - - -
459B ASN 4.4 3.8 + - - -
460B VAL* 1.3 78.3 - - - +
462B LEU* 1.3 65.4 + - - +
463B SER* 4.2 4.7 + - - -
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Residues in contact with LEU 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B VAL* 4.4 13.2 - - + -
218B THR 3.4 5.4 - - - +
219B LEU* 3.7 35.0 - - + +
295B ILE* 4.2 12.6 - - + -
414B ILE* 4.9 0.9 - - + -
443B LEU* 4.0 15.5 - - + +
445B ILE* 3.1 48.5 - - + +
447B LEU* 3.9 24.5 - - + +
461B SER* 1.3 76.5 - - - +
463B SER* 1.3 60.9 + - - +
464B VAL* 5.3 0.3 - - - +
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Residues in contact with SER 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B ASP 4.0 1.2 - - - +
217B VAL* 3.7 3.5 - - - +
218B THR* 3.0 32.5 + - - -
220B ARG* 3.6 34.8 + - - -
443B LEU* 4.8 0.2 - - - -
461B SER* 4.2 3.8 + - - -
462B LEU* 1.3 76.0 - - - +
464B VAL* 1.3 63.9 + - - +
465B THR* 4.2 12.6 - - - -
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Residues in contact with VAL 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B TYR* 4.6 17.3 - - + -
216B ASP 4.0 4.9 - - - +
217B VAL* 4.7 6.1 - - + -
441B LEU* 3.9 39.5 - - + +
443B LEU* 3.4 42.4 - - + +
462B LEU 5.3 0.4 - - - +
463B SER* 1.3 73.3 - - - +
465B THR* 1.3 68.6 + - - +
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Residues in contact with THR 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B TYR* 3.2 8.7 - - - -
216B ASP* 2.8 48.8 + - - +
218B THR* 6.4 1.6 - - - -
220B ARG* 6.0 2.0 - - - +
463B SER* 4.6 11.2 - - - -
464B VAL* 1.3 85.6 - - - +
466B PRO* 1.3 73.7 + - - +
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Residues in contact with PRO 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B GLY 3.6 3.1 - - - +
215B TYR* 3.2 30.5 - - + +
216B ASP* 3.8 2.9 - - - +
465B THR* 1.3 90.7 + - - +
467B ALA* 1.3 68.5 + - - +
468B ALA* 3.4 8.1 + - + +
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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