Contacts of the strand formed by residues 458 - 466 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221A GLY* 3.3 1.6 - - - -
222A ASP* 2.9 61.6 + - - +
223A THR* 5.3 1.2 - - - +
453A SER* 3.0 29.0 + - - +
456A GLY* 4.5 9.9 + - - -
457A PHE* 1.3 75.0 - - - +
459A ASN* 1.3 76.4 + - - +
460A VAL* 2.9 5.9 + - - +
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Residues in contact with ASN 459 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220A ARG* 3.3 11.1 - - - +
221A GLY* 3.4 5.8 - - - -
222A ASP* 2.5 28.8 - - - +
458A ASN* 1.3 74.6 - - - +
460A VAL* 1.3 63.1 + - - +
461A SER* 3.5 5.8 + - - -
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Residues in contact with VAL 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A VAL* 6.4 1.1 - - + -
219A LEU* 3.7 23.3 - - + -
220A ARG 3.3 5.8 - - - +
221A GLY* 4.7 4.0 - - - -
222A ASP 5.2 0.2 - - - +
277A LEU* 5.4 6.5 - - + -
297A LEU* 6.1 2.9 - - + -
447A LEU* 3.6 19.1 - - + +
449A ALA* 5.5 9.1 - - - +
452A LEU* 3.9 28.0 - - + -
457A PHE* 3.7 37.0 - - + +
458A ASN 3.5 11.4 - - - +
459A ASN* 1.3 76.9 - - - +
461A SER* 1.3 62.5 + - - +
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Residues in contact with SER 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A THR 3.7 0.5 - - - +
219A LEU* 3.2 5.2 - - - +
220A ARG* 2.9 54.6 + - - +
447A LEU* 4.0 6.5 - - - -
459A ASN 3.5 5.0 + - - -
460A VAL* 1.3 76.0 - - - +
462A LEU* 1.3 65.1 + - - +
463A SER* 4.4 4.4 + - - -
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Residues in contact with LEU 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A VAL* 4.9 1.8 - - + -
217A VAL* 4.6 13.7 - - + -
218A THR 3.2 5.6 - - - +
219A LEU* 3.2 42.8 - - + +
293A VAL* 6.5 0.2 - - + -
295A ILE* 4.2 15.3 - - + -
414A ILE* 4.7 1.8 - - + -
443A LEU* 3.8 22.9 - - + +
445A ILE* 3.0 36.3 - - + -
447A LEU* 4.4 21.9 - - + +
461A SER* 1.3 78.4 - - - +
463A SER* 1.3 61.6 + - - +
464A VAL 4.1 0.3 + - - -
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Residues in contact with SER 463 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216A ASP 3.2 4.5 - - - +
217A VAL* 3.4 1.8 - - - +
218A THR* 2.6 58.4 + - - +
220A ARG* 3.9 17.2 + - - -
443A LEU* 4.9 0.9 - - - -
461A SER* 4.4 4.5 + - - -
462A LEU* 1.3 74.3 - - - +
464A VAL* 1.3 62.1 + - - +
465A THR* 3.8 16.4 - - - -
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Residues in contact with VAL 464 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215A TYR* 4.5 16.2 - - + -
216A ASP 3.7 3.6 - - - +
217A VAL* 4.6 8.1 - - + +
441A LEU* 3.0 45.5 - - + +
442A ARG* 4.8 0.2 - - - -
443A LEU* 3.1 46.0 - - + +
462A LEU 4.1 0.6 + - - -
463A SER* 1.3 70.3 - - - +
465A THR* 1.3 65.7 + - - +
466A PRO* 4.6 0.9 - - - +
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Residues in contact with THR 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A TYR* 3.6 5.4 - - - -
216A ASP* 2.7 47.4 + - - +
218A THR* 4.9 6.1 - - + +
220A ARG* 5.9 1.8 - - - +
463A SER* 3.8 22.7 - - - -
464A VAL* 1.3 81.4 - - - +
466A PRO* 1.3 76.8 + - + +
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Residues in contact with PRO 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A GLY 3.6 1.6 - - - +
215A TYR* 3.2 29.2 - - + -
216A ASP* 4.7 1.4 - - - +
464A VAL 4.6 1.1 - - - +
465A THR* 1.3 98.8 + - + +
467A ALA* 1.3 69.3 + - - +
468A ALA* 3.6 5.9 + - + +
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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