Contacts of the strand formed by residues 485 - 493 (chain D) in PDB entry 2C11
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 ILE 485 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335D TRP* 3.6 30.3 - - + -
352D VAL* 3.9 10.1 - - + -
359D LEU* 4.4 6.7 - - + -
360D VAL* 4.4 20.0 - - + -
363D ILE* 4.5 6.1 - - + -
477D THR* 4.6 3.4 - - + -
478D VAL 3.6 7.4 - - - +
479D PHE* 3.8 26.7 - - + -
483D GLY 4.4 1.6 - - - +
484D ALA* 1.3 73.4 - - - +
486D GLU* 1.3 73.1 + - - +
487D ILE* 4.3 12.1 - - + -
603D TYR* 5.7 0.7 - - + -
703D PHE 4.0 0.3 - - - +
704D PHE* 3.4 4.6 - - - -
705D LEU* 2.8 60.1 + - + +
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Residues in contact with GLU 486 (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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476D ASP 4.5 0.2 - - - -
477D THR* 3.6 0.2 - - - -
478D VAL* 2.8 43.0 + - + +
480D HIS* 2.9 30.4 + - - +
485D ILE* 1.3 72.8 - - - +
487D ILE* 1.3 77.4 + - - +
488D ARG* 2.9 46.3 + - + +
703D PHE 3.6 5.8 - - - +
704D PHE* 3.2 34.2 - - + -
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Residues in contact with ILE 487 (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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363D ILE* 4.0 21.3 - - + -
476D ASP 3.4 4.3 - - - +
477D THR* 3.7 27.6 - - + +
485D ILE* 4.3 10.5 - - + +
486D GLU* 1.3 86.0 - - - +
488D ARG* 1.3 66.9 + - - +
526D PHE* 3.7 35.0 - - + -
702D GLY* 3.0 5.7 - - - -
703D PHE* 2.9 67.5 + - + +
705D LEU* 5.3 0.4 - - + -
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Residues in contact with ARG 488 (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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488C ARG* 4.8 14.3 - - - +
475D TRP* 3.9 0.9 - - - -
476D ASP* 2.7 45.1 + - + +
478D VAL* 5.1 3.4 - - + -
486D GLU* 2.9 37.2 + - + +
487D ILE* 1.3 86.5 - - - +
489D PHE* 1.3 61.0 + - - +
490D TYR* 3.9 32.4 + - + +
526D PHE* 5.5 0.5 - - - -
608D LEU* 2.8 41.8 - - - +
700D GLY* 3.6 22.6 + - - -
701D VAL 3.6 4.9 - - - +
702D GLY* 4.3 4.3 - - - +
704D PHE* 4.4 4.8 - - - -
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Residues in contact with PHE 489 (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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473D TYR* 3.7 29.6 - + + -
474D VAL 3.0 7.0 - - - -
475D TRP* 3.3 37.5 - + + -
488D ARG* 1.3 78.4 - - - +
490D TYR* 1.3 69.8 - - - +
491D ALA* 4.6 5.2 - - + -
522D HIS* 4.7 16.8 - - + -
523D SER 4.8 0.7 - - - -
524D ALA* 3.7 34.1 - - + -
526D PHE* 4.3 10.1 - + + -
680D ALA* 4.2 7.6 - - + -
681D GLY* 5.0 0.9 - - - -
682D PHE* 4.8 4.2 - + - -
699D ASN 4.0 1.9 - - - +
700D GLY* 3.8 0.2 - - - -
701D VAL* 3.1 55.5 + - + -
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Residues in contact with TYR 490 (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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438C LEU* 3.7 39.9 - - + +
472D ASP 3.8 0.7 - - - +
473D TYR* 3.4 6.2 - - - -
474D VAL* 3.0 45.1 + - + +
476D ASP* 4.4 8.8 + - + -
488D ARG* 3.9 42.2 + - + +
489D PHE* 1.3 83.2 - - - +
491D ALA* 1.3 61.9 + - - +
492D THR 3.9 0.2 - - - -
696D THR* 3.5 44.9 - - + -
697D VAL* 6.0 0.2 - - - -
698D GLY 5.9 0.2 - - - -
699D ASN 4.5 4.9 - - - +
700D GLY* 3.4 27.4 - - - +
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Residues in contact with ALA 491 (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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471D PAQ 5.0 6.7 - - + +
472D ASP 4.0 2.9 - - - -
473D TYR* 4.6 14.6 - - + -
489D PHE* 4.6 3.8 - - + -
490D TYR* 1.3 73.4 - - - +
492D THR* 1.3 59.8 - - - +
522D HIS* 4.1 31.6 - - + +
682D PHE* 4.5 15.1 - - + -
684D HIS* 6.2 0.2 - - - +
694D THR* 3.9 11.9 - - - +
695D VAL 3.8 13.9 - - - +
699D ASN* 5.0 9.4 + - - +
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Residues in contact with THR 492 (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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439C PRO* 5.9 0.9 - - + -
441C ARG* 3.5 3.6 - - - -
442C ARG* 3.1 37.6 + - + +
471D PAQ 2.9 12.2 - - - +
472D ASP* 2.9 37.5 + - + +
474D VAL* 3.9 19.5 - - + -
491D ALA* 1.3 73.5 - - - +
493D GLY* 1.3 69.3 + - - +
694D THR* 2.9 22.8 + - - -
696D THR* 4.0 17.3 - - + -
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Residues in contact with GLY 493 (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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442C ARG 3.7 0.4 - - - -
443C HIS* 4.2 1.1 - - - -
472D ASP* 3.2 19.1 - - - -
492D THR* 1.3 86.6 + - - +
494D TYR* 1.3 61.7 + - - -
692D PRO 4.1 0.2 - - - +
693D ASN* 3.0 26.5 + - - -
694D THR* 2.8 28.3 + - - -
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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