Contacts of the helix formed by residues 461 - 471 (chain C) in PDB entry 1EQQ
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 GLY 461 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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427C GLY* 5.7 2.9 - - - -
428C ALA* 3.7 15.6 + - - +
460C PHE* 1.3 81.6 - - - +
462C LYS* 1.3 66.1 + - - +
464C ALA* 2.9 15.4 + - - +
465C GLU* 3.2 10.8 + - - +
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Residues in contact with LYS 462 (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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460C PHE 3.3 0.2 + - - -
461C GLY* 1.3 68.2 - - - -
463C LEU* 1.3 79.2 + - + +
465C GLU* 2.6 42.3 + - - +
466C VAL* 2.7 27.8 + - + +
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Residues in contact with LEU 463 (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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459C LEU* 4.0 13.8 - - + +
460C PHE 3.3 10.5 + - - +
462C LYS* 1.3 96.8 - - + +
464C ALA* 1.3 65.4 + - - +
466C VAL* 3.1 13.5 + - + +
467C ALA* 2.7 26.5 + - - +
502C VAL* 5.6 4.5 - - + +
507C GLY* 4.6 8.5 - - - -
508C THR* 3.0 52.0 - - + +
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Residues in contact with ALA 464 (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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420C VAL* 4.6 2.8 - - + +
428C ALA* 4.0 15.5 - - + +
429C VAL 4.1 0.7 - - - +
430C ALA* 3.7 25.0 - - - +
459C LEU* 3.7 13.1 - - - +
460C PHE* 3.0 24.9 + - - -
461C GLY 2.9 16.6 + - - +
463C LEU* 1.3 78.3 - - - +
465C GLU* 1.3 60.4 + - - +
467C ALA* 3.2 4.0 - - - +
468C SER* 3.0 20.2 + - - -
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Residues in contact with GLU 465 (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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420C VAL* 5.4 2.0 - - - -
422C TYR* 4.7 20.6 + - + +
428C ALA* 4.8 12.6 - - + +
461C GLY 3.7 11.4 - - - +
462C LYS* 2.6 25.0 + - - +
464C ALA* 1.3 68.6 - - - +
466C VAL* 1.3 69.1 + - + +
468C SER* 2.7 19.2 + - - -
469C GLU* 2.8 28.9 + - - +
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Residues in contact with VAL 466 (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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462C LYS* 2.7 47.2 + - + +
463C LEU* 3.4 17.9 - - + +
465C GLU* 1.3 72.7 - - + +
467C ALA* 1.3 66.4 + - - +
469C GLU* 3.0 6.8 + - - +
470C TYR* 2.9 36.7 + - + +
471C LEU* 4.0 0.4 + - - -
508C THR* 5.4 4.3 - - + -
510C GLN* 4.6 12.3 - - - +
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Residues in contact with ALA 467 (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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418C PRO* 4.1 3.0 - - + +
430C ALA* 4.3 5.2 - - + -
432C ILE* 4.5 4.7 - - + -
459C LEU* 3.2 35.9 - - + -
463C LEU 2.7 9.2 + - - +
464C ALA 3.2 8.1 - - - +
466C VAL* 1.3 72.3 - - - +
468C SER* 1.3 59.0 + - - +
471C LEU* 2.6 58.6 + - + +
472C ARG* 3.6 0.9 + - - -
508C THR* 5.5 2.6 - - + +
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Residues in contact with SER 468 (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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418C PRO* 4.9 3.3 - - - +
420C VAL* 3.1 47.9 - - - +
422C TYR* 5.1 5.0 + - - -
464C ALA 3.0 3.6 + - - -
465C GLU* 2.7 17.6 + - - -
467C ALA* 1.3 76.2 - - - +
469C GLU* 1.3 59.3 + - - +
471C LEU 4.9 0.2 - - - +
472C ARG* 2.7 15.6 + - - -
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Residues in contact with GLU 469 (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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465C GLU* 2.8 34.4 + - - +
466C VAL* 3.9 2.7 - - - +
468C SER* 1.3 72.3 - - - +
470C TYR* 1.3 105.6 + - + +
472C ARG* 2.8 17.0 + - - -
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Residues in contact with TYR 470 (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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466C VAL* 2.9 24.7 + - + +
469C GLU* 1.3 123.1 + - + +
471C LEU* 1.3 60.1 + - - +
472C ARG* 2.8 26.3 + - - +
475C SER* 4.3 1.6 + - - -
510C GLN* 3.6 27.3 + - - +
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Residues in contact with LEU 471 (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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414C LEU* 3.7 20.6 - - + -
418C PRO* 3.1 29.4 - - + +
432C ILE* 4.0 9.9 - - + -
459C LEU* 4.9 0.2 - - + -
466C VAL* 6.2 0.2 - - + -
467C ALA* 2.6 45.5 + - + +
470C TYR* 1.3 71.2 - - - +
472C ARG* 1.3 67.5 + - - +
475C SER* 3.8 8.3 - - - +
477C VAL* 3.5 36.1 - - + -
508C THR* 4.6 7.4 - - + +
510C GLN* 3.0 34.8 - - + +
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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