Contacts of the helix formed by residues 492 - 503 (chain C) in PDB entry 1EQR
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 492 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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459C ALA* 5.7 2.6 - - - +
490C ILE* 3.4 5.0 - - + +
491C HIS* 1.3 88.0 - - + +
493C GLY* 1.3 66.1 + - - +
494C ASP* 2.8 32.4 + - - +
495C MET* 3.0 24.1 + - + +
496C GLN* 3.0 18.0 + - - +
521C LEU* 4.5 2.5 - - - -
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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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491C HIS 4.2 0.4 + - - -
492C ASN* 1.3 73.4 - - - +
494C ASP* 1.3 61.6 + - - -
496C GLN* 2.9 14.6 + - - +
497C GLN* 3.0 21.4 + - - +
518C LEU* 4.6 4.6 - - - +
521C LEU* 3.8 35.9 + - - +
522C LYS* 6.5 1.1 - - - -
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Residues in contact with ASP 494 (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 ALA* 5.5 3.6 - - + -
492C ASN* 2.8 16.6 + - - +
493C GLY* 1.3 71.1 - - - -
495C MET* 1.3 64.9 + - - +
497C GLN* 3.3 15.1 + - - +
498C THR* 3.2 21.7 + - - -
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Residues in contact with MET 495 (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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453C SER* 5.5 0.4 - - - -
454C PRO* 3.3 36.6 - - + -
457C MET 3.9 15.9 - - - +
458C THR* 4.4 0.7 - - - -
459C ALA* 3.9 32.0 - - + +
462C LEU* 4.3 12.1 - - + -
490C ILE* 3.3 28.5 - - + -
492C ASN* 3.0 29.8 + - + +
494C ASP* 1.3 78.4 - - - +
496C GLN* 1.3 58.3 + - - +
498C THR* 2.8 25.1 + - - -
499C VAL* 3.1 11.8 + - - +
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Residues in contact with GLN 496 (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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199C GLN* 5.4 0.3 - - - +
450C PRO 2.6 26.8 + - - -
451C PHE* 3.0 35.4 - - + +
490C ILE* 3.7 22.6 - - + +
492C ASN 3.0 10.8 + - - +
493C GLY 2.9 9.7 + - - +
495C MET* 1.3 76.7 - - - +
497C GLN* 1.3 58.6 - - - +
499C VAL* 3.9 3.0 + - - +
500C PHE* 3.3 46.4 + - + -
517C LEU* 4.6 3.4 - - + +
518C LEU* 4.2 9.0 - - + -
521C LEU* 3.9 17.9 - - + +
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Residues in contact with GLN 497 (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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493C GLY 3.0 17.7 + - - +
494C ASP* 3.7 17.5 + - - +
495C MET 3.0 0.4 - - - -
496C GLN* 1.3 75.4 - - - +
498C THR* 1.3 67.5 + - - +
500C PHE* 3.1 7.9 + - - +
501C GLY* 2.9 20.3 + - - -
507C GLU* 5.0 10.7 - - - +
510C GLN* 3.3 26.1 + - - +
518C LEU* 4.0 23.2 - - + +
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Residues in contact with THR 498 (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 ALA* 3.9 32.6 + - - +
462C LEU* 4.5 4.3 - - + -
463C LYS* 4.1 24.4 + - + +
494C ASP 3.2 12.7 + - - -
495C MET* 2.8 13.4 + - - -
497C GLN* 1.3 77.4 - - - +
499C VAL* 1.3 58.2 + - - +
501C GLY* 3.0 3.9 + - - -
502C ILE* 2.8 52.0 + - + +
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Residues in contact with VAL 499 (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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435C MET* 4.2 10.3 - - + -
436C PHE* 4.0 12.3 - - + -
450C PRO* 3.5 19.7 - - + +
452C THR 5.3 0.4 - - - +
454C PRO* 5.4 0.2 - - + -
462C LEU* 3.9 22.0 - - + -
490C ILE* 3.7 24.7 - - + -
495C MET* 3.1 9.5 + - - +
496C GLN* 3.9 8.7 - - - +
498C THR* 1.3 77.3 - - - +
500C PHE* 1.3 51.6 + - - +
502C ILE* 3.1 10.5 + - - +
503C LEU* 2.6 57.4 + - + +
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Residues in contact with PHE 500 (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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450C PRO* 4.2 13.0 - - + -
451C PHE* 3.8 10.8 - + - -
496C GLN* 3.3 48.4 + - + -
497C GLN* 3.1 10.4 + - - +
499C VAL* 1.3 79.8 - - - +
501C GLY* 1.3 63.8 + - - +
503C LEU* 2.9 11.3 + - + -
505C ILE* 3.0 37.6 + - + +
510C GLN* 3.3 39.9 - - + +
514C PHE* 3.4 41.7 - + + -
517C LEU* 4.8 0.4 - - + -
518C LEU* 3.9 20.2 - - + -
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Residues in contact with GLY 501 (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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463C LYS* 6.2 5.8 - - - -
497C GLN 2.9 13.5 + - - -
498C THR* 3.5 3.6 - - - -
500C PHE* 1.3 74.2 - - - +
502C ILE* 1.3 63.5 + - - +
504C GLY* 2.8 15.5 + - - -
505C ILE 4.5 7.6 - - - -
506C ASN* 6.0 0.4 - - - -
510C GLN* 4.2 3.5 - - - +
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Residues in contact with ILE 502 (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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436C PHE* 3.6 17.0 - - + -
443C GLY* 5.7 0.3 - - - -
444C LEU* 3.9 22.5 + - + +
462C LEU* 3.5 37.5 - - + +
463C LYS* 4.4 12.6 - - + -
466C PRO* 3.5 27.6 - - + -
498C THR* 2.8 44.6 + - + +
499C VAL* 3.3 7.9 - - - +
501C GLY* 1.3 75.8 - - - +
503C LEU* 1.3 58.1 + - - +
504C GLY* 2.9 6.9 + - - -
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Residues in contact with LEU 503 (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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436C PHE* 3.4 33.2 - - + -
444C LEU* 3.8 13.5 - - + +
445C THR* 3.7 11.9 - - - +
446C ALA* 3.6 20.0 - - + +
450C PRO* 3.5 29.8 - - + -
499C VAL* 2.6 43.9 + - + +
500C PHE* 2.9 6.9 + - + +
502C ILE* 1.3 70.6 - - - +
504C GLY* 1.3 55.2 + - - +
505C ILE* 2.9 22.0 + - + +
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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