Contacts of the helix formed by residues 493 - 505 (chain C) in PDB entry 2IHU
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 493 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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438C PHE* 4.8 2.3 - - - -
464C GLY* 3.4 15.6 - - - -
492C THR* 1.3 71.9 - - - +
494C GLY* 1.3 62.8 - - - +
495C LEU 3.5 2.0 - - - -
496C ILE* 3.2 23.0 + - + +
497C GLU 3.1 17.0 + - - -
511C ALA 4.8 2.8 + - - -
512C VAL* 3.0 19.1 + - - +
514C PHE* 3.3 31.4 - - - -
600C TP8 3.5 33.6 - - + +
33D VAL* 4.4 5.9 - - - +
34D VAL 4.8 3.0 + - - +
53D LEU* 4.1 18.6 - - - +
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Residues in contact with GLY 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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412C PHE* 4.7 3.6 - - - -
490C ASN* 4.4 0.9 - - - -
492C THR* 3.1 14.0 + - - -
493C ASN* 1.3 70.2 - - - +
495C LEU* 1.3 65.9 + - - +
497C GLU* 3.0 7.4 + - - +
498C LEU* 2.9 21.4 + - - +
561C TYR* 4.3 15.9 - - - -
600C TP8 2.9 23.7 + - - -
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Residues in contact with LEU 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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271C TYR* 3.7 29.8 - - + -
410C ILE* 5.6 1.1 - - + -
411C GLY* 3.9 20.2 - - - +
412C PHE* 3.6 15.2 - - + +
414C ARG* 6.3 0.2 - - - +
415C HIS* 4.6 4.7 - - - +
493C ASN 3.5 0.2 - - - -
494C GLY* 1.3 72.6 - - - +
496C ILE* 1.3 57.2 + - - +
498C LEU* 3.3 16.2 + - + +
499C TYR* 3.0 47.4 + - + -
600C TP8 2.8 72.4 + - + +
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Residues in contact with ILE 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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493C ASN* 3.4 23.1 - - + +
494C GLY 3.1 0.8 - - - -
495C LEU* 1.3 76.7 - - - +
497C GLU* 1.3 57.5 + - - +
499C TYR* 3.1 8.3 + - + +
500C GLN* 3.0 27.8 + - - +
511C ALA 4.8 0.9 - - - +
512C VAL* 3.7 17.3 - - + -
600C TP8 3.5 46.4 - - + +
34D VAL* 3.4 23.3 - - + +
35D GLY* 3.4 36.6 - - - +
36D ARG 4.1 0.4 - - - +
38D ALA* 3.7 10.8 - - + -
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Residues in contact with GLU 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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490C ASN* 5.5 1.6 + - - -
492C THR* 3.5 8.4 - - + +
493C ASN 3.1 10.5 + - - +
494C GLY* 3.0 10.6 + - - +
496C ILE* 1.3 74.0 - - - +
498C LEU* 1.3 63.3 + - - +
500C GLN* 3.2 17.1 + - - +
501C ASN* 2.8 33.1 + - - +
507C SER* 3.0 31.0 + - - +
509C ASP* 4.8 0.3 - - - +
512C VAL* 3.7 11.3 - - + +
513C LYS* 3.1 35.5 + - - -
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Residues in contact with LEU 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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271C TYR* 3.7 38.1 - - + +
412C PHE* 4.0 23.8 - - + -
494C GLY 2.9 11.9 + - - +
495C LEU* 3.3 14.1 - - + +
497C GLU* 1.3 76.1 - - - +
499C TYR* 1.3 57.5 + - - +
501C ASN* 3.2 12.9 + - + +
502C ILE* 2.9 47.4 + - + +
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Residues in contact with TYR 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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271C TYR* 3.3 22.3 + - - -
495C LEU* 3.0 51.6 + - + -
496C ILE* 3.1 11.2 + - + +
498C LEU* 1.3 71.4 - - - +
500C GLN* 1.3 65.7 + - - +
502C ILE* 3.9 13.8 - - + -
503C GLY 3.0 19.4 + - - -
600C TP8 2.5 27.9 + - - -
36D ARG* 3.6 52.1 - - + +
38D ALA* 4.2 4.5 - - + -
39D ALA* 3.4 25.3 - - + +
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Residues in contact with GLN 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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496C ILE 3.0 14.9 + - - +
497C GLU* 3.2 10.4 + - - +
499C TYR* 1.3 74.8 - - - +
501C ASN* 1.3 52.6 - - - +
504C HIS* 2.8 35.7 + - - +
506C ARG 3.3 19.6 - - - +
507C SER* 3.5 4.6 - - - -
508C HIS* 2.9 50.2 + - - +
511C ALA* 3.6 19.4 - - - +
512C VAL* 3.7 23.3 - - - +
38D ALA* 3.8 22.7 - - + +
41D ILE 5.5 0.2 + - - -
42D LEU* 3.7 16.3 + - + +
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Residues in contact with ASN 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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497C GLU* 2.8 32.3 + - - +
498C LEU* 3.6 13.6 - - + +
500C GLN* 1.3 72.7 - - - +
502C ILE* 1.3 62.7 + - - +
505C HIS* 3.0 30.7 + - - -
506C ARG* 3.6 25.3 + - - +
507C SER* 3.3 20.2 + - - -
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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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271C TYR* 3.9 21.3 - - + +
498C LEU* 2.9 48.0 + - + +
499C TYR* 3.4 16.8 + - + +
501C ASN* 1.3 77.2 - - + +
503C GLY* 1.3 62.0 + - - +
505C HIS* 4.3 13.8 + - - -
39D ALA* 5.4 3.8 - - + -
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Residues in contact with GLY 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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499C TYR 3.0 14.2 + - - -
502C ILE* 1.3 79.8 - - - +
504C HIS* 1.3 67.7 + - - +
505C HIS* 5.4 3.0 - - - -
39D ALA* 3.4 27.2 - - - +
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Residues in contact with HIS 504 (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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500C GLN 2.8 18.9 + - - +
503C GLY* 1.3 78.0 + - - +
505C HIS* 1.3 76.0 + - - +
506C ARG* 3.2 17.1 + - + +
38D ALA 2.8 29.8 + - - -
39D ALA* 3.4 9.4 - - - -
40D SER* 3.8 19.3 - - - -
41D ILE* 3.4 9.6 + - - -
42D LEU* 3.5 44.4 + - + +
45D GLU* 4.2 5.8 - - - -
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Residues in contact with HIS 505 (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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501C ASN* 3.0 25.6 + - - +
502C ILE* 4.3 15.3 + - - -
503C GLY 5.4 2.0 - - - -
504C HIS* 1.3 81.6 - - - +
506C ARG* 1.3 61.7 + - - +
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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