Contacts of the strand formed by residues 485 - 493 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335C TRP* 3.5 22.0 - - + -
352C VAL* 3.8 28.3 - - + -
359C LEU* 4.0 13.9 - - + -
360C VAL* 4.1 19.1 - - + -
363C ILE* 4.6 8.5 - - + -
477C THR* 4.5 5.2 - - - +
478C VAL 3.5 10.3 - - - +
479C PHE* 3.9 22.7 - - + -
483C GLY 4.6 0.2 - - - +
484C ALA* 1.3 72.2 - - - +
486C GLU* 1.3 66.0 + - - +
487C ILE* 4.1 8.6 + - + +
530C LEU* 5.8 0.2 - - + -
603C TYR* 5.1 0.9 - - + -
703C PHE 4.1 0.2 - - - +
704C PHE* 3.5 1.9 - - - -
705C LEU* 2.8 52.0 + - + +
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Residues in contact with GLU 486 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476C ASP* 5.4 1.0 - - - +
478C VAL* 2.8 46.8 + - + +
480C HIS* 3.5 24.8 + - - +
484C ALA 4.0 1.0 - - - -
485C ILE* 1.3 73.5 - - - +
487C ILE* 1.3 72.0 + - - +
488C ARG* 3.4 41.6 + - + +
490C TYR* 5.2 0.5 + - - -
703C PHE 3.4 8.5 - - - +
704C PHE* 3.2 45.5 - - + -
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Residues in contact with ILE 487 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363C ILE* 4.3 21.8 - - + -
476C ASP 3.7 7.4 - - - +
477C THR* 3.3 27.8 - - - +
485C ILE* 4.6 11.9 - - + +
486C GLU* 1.3 85.3 - - - +
488C ARG* 1.3 64.6 + - - +
526C PHE* 3.8 31.4 - - + -
702C GLY* 2.9 6.5 - - - -
703C PHE* 2.8 72.4 + - + +
705C LEU* 5.7 0.2 - - + -
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Residues in contact with ARG 488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475C TRP* 3.9 0.3 - - - -
476C ASP* 2.7 46.0 + - + +
486C GLU* 3.4 34.8 + - + +
487C ILE* 1.3 78.3 - - - +
489C PHE* 1.3 59.5 + - - +
490C TYR* 3.6 32.1 + - + +
526C PHE* 5.6 0.4 - - - -
608C LEU* 3.6 28.6 - - + +
700C GLY 3.6 20.5 + - - -
701C VAL 3.1 13.0 - - - +
702C GLY* 4.4 1.1 - - - +
704C PHE* 3.7 13.1 - - - -
488D ARG* 4.8 14.8 - - - +
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Residues in contact with PHE 489 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473C TYR* 3.8 25.1 - + - -
474C VAL 2.9 7.0 - - - -
475C TRP* 3.1 38.4 - + + -
488C ARG* 1.3 75.5 - - - +
490C TYR* 1.3 78.5 + - - +
491C ALA* 4.6 4.7 - - + -
522C HIS* 4.9 6.3 - - + -
523C SER 4.7 3.6 - - - -
524C ALA* 3.4 24.5 - - + -
526C PHE* 3.8 22.2 - + + -
680C ALA* 3.6 11.2 - - + -
681C GLY* 5.2 0.2 - - - -
682C PHE* 4.7 10.5 - + - -
699C ASN 4.1 0.9 - - - +
700C GLY* 3.5 0.3 - - - -
701C VAL* 2.8 56.2 + - + +
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Residues in contact with TYR 490 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473C TYR* 3.2 8.0 - - - +
474C VAL* 2.8 50.5 + - + -
476C ASP* 3.7 24.9 + - - -
486C GLU* 5.2 0.2 + - - -
488C ARG* 3.6 35.6 + - + +
489C PHE* 1.3 85.0 - - - +
491C ALA* 1.3 61.2 + - - +
492C THR 4.2 0.2 - - - -
696C THR* 3.4 38.6 - - + -
698C GLY 5.7 0.4 - - - -
699C ASN* 4.2 6.3 - - + +
700C GLY* 3.1 31.0 - - - -
438D LEU* 3.5 30.0 - - + +
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Residues in contact with ALA 491 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471C PAQ 4.7 6.1 - - + +
472C ASP 3.8 3.6 - - - -
473C TYR* 4.4 12.8 - - + -
489C PHE* 4.6 2.7 - - + -
490C TYR* 1.3 76.6 - - - +
492C THR* 1.3 61.2 + - - +
522C HIS* 4.2 35.9 - - + +
682C PHE* 4.5 9.6 - - + -
694C THR* 3.9 18.3 - - + +
695C VAL 4.3 6.2 - - - +
696C THR* 5.1 0.2 - - - -
699C ASN* 4.6 8.6 + - - +
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Residues in contact with THR 492 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471C PAQ 2.8 30.1 - - - +
472C ASP* 2.9 26.5 + - + +
474C VAL* 4.4 14.6 - - + -
491C ALA* 1.3 74.4 - - - +
493C GLY* 1.3 67.4 + - - +
494C TYR 3.9 0.9 - - - +
694C THR* 2.5 31.5 + - - -
696C THR* 4.5 12.8 - - + -
441D ARG* 3.6 2.8 - - - +
442D ARG* 3.1 40.7 + - + +
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Residues in contact with GLY 493 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472C ASP* 2.9 18.8 - - - -
492C THR* 1.3 86.9 + - - +
494C TYR* 1.3 60.0 + - - -
693C ASN* 2.9 40.2 + - - -
694C THR 3.1 6.1 + - - -
442D ARG 3.2 7.6 - - - -
443D HIS* 3.8 4.3 - - - -
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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