Contacts of the helix formed by residues 493 - 505 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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438A PHE* 4.7 2.2 - - - -
464A GLY* 3.3 15.8 - - - -
492A THR* 1.3 71.4 - - - +
494A GLY* 1.3 64.9 + - - +
495A LEU 3.5 1.8 - - - -
496A ILE* 3.1 22.3 + - + +
497A GLU 3.1 9.9 + - - -
511A ALA 4.8 2.4 + - - -
512A VAL* 2.9 19.2 + - - +
514A PHE* 3.2 32.6 - - - -
600A TP9 3.4 37.9 - - + +
33B VAL* 4.1 7.1 - - - +
34B VAL 4.7 2.8 + - - -
53B LEU* 4.0 18.0 - - - +
54B THR 5.5 0.2 + - - -
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Residues in contact with GLY 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412A PHE* 4.7 1.8 - - - -
490A ASN* 4.4 9.6 - - - -
492A THR* 3.1 11.6 + - - -
493A ASN* 1.3 68.1 - - - +
495A LEU* 1.3 65.4 + - - +
497A GLU* 3.0 7.1 + - - +
498A LEU 3.0 17.7 + - - -
561A TYR* 4.5 5.8 - - - -
563A PHE* 3.8 13.5 - - - -
600A TP9 2.9 25.1 + - - -
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Residues in contact with LEU 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A TYR* 3.5 40.4 - - + +
411A GLY 3.9 15.5 - - - +
412A PHE* 3.6 27.5 - - + +
415A HIS* 4.8 2.2 - - + +
493A ASN 3.5 0.4 - - - -
494A GLY* 1.3 72.4 - - - +
496A ILE* 1.3 59.9 + - + +
498A LEU* 3.1 15.0 + - + +
499A TYR* 3.1 39.3 + - + -
600A TP9 2.7 33.1 + - - +
603A TAR 3.4 32.3 - - - +
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Residues in contact with ILE 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493A ASN* 3.1 13.5 + - + +
495A LEU* 1.3 81.7 - - + +
497A GLU* 1.3 60.5 + - - +
499A TYR* 3.2 5.9 + - + +
500A GLN* 3.0 26.9 + - - +
511A ALA 4.8 0.4 - - - +
512A VAL* 3.6 17.9 - - + -
600A TP9 3.7 35.0 - - + +
603A TAR 4.9 2.2 - - - +
34B VAL* 3.3 29.6 - - + +
35B GLY* 3.5 38.8 - - - +
36B ARG* 3.8 5.8 - - + +
38B ALA* 3.6 10.5 - - + +
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Residues in contact with GLU 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490A ASN* 5.5 1.4 + - - -
492A THR* 3.4 9.1 - - + +
493A ASN 3.1 9.0 + - - +
494A GLY* 3.0 9.6 + - - +
496A ILE* 1.3 72.5 - - - +
498A LEU* 1.3 66.1 + - - +
500A GLN* 3.3 12.5 + - - +
501A ASN* 2.9 33.0 + - - +
507A SER* 2.8 35.6 + - - +
509A ASP* 4.5 0.7 - - - +
512A VAL* 3.7 11.8 - - + +
513A LYS* 3.2 34.2 + - - -
563A PHE* 4.3 15.6 - - + -
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Residues in contact with LEU 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A TYR* 4.4 4.7 - - + -
412A PHE* 3.9 28.9 - - + -
494A GLY 3.0 11.7 + - - +
495A LEU* 3.2 23.8 - - + +
497A GLU* 1.3 75.9 - - - +
499A TYR* 1.3 58.4 + - + +
501A ASN* 3.1 6.2 + - + +
502A ILE* 2.9 47.0 + - + +
563A PHE* 3.7 42.3 - - + -
565A PRO* 4.4 8.3 - - + -
568A PHE* 3.8 30.3 - - + -
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Residues in contact with TYR 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A TYR* 2.4 36.1 + + - -
495A LEU* 3.1 41.1 + - + -
496A ILE* 3.2 10.0 + - + +
498A LEU* 1.3 72.3 - - + +
500A GLN* 1.3 65.4 + - - +
502A ILE* 3.4 14.4 + - + +
503A GLY 2.9 19.8 + - - -
571A LEU* 3.8 24.0 - - + +
603A TAR 4.2 5.6 + - - -
36B ARG* 3.7 58.2 - - + +
38B ALA* 4.3 2.0 - - + -
39B ALA* 3.3 26.1 - - + +
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Residues in contact with GLN 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496A ILE 3.0 16.7 + - - +
497A GLU* 3.4 9.4 - - - +
499A TYR* 1.3 74.8 - - - +
501A ASN* 1.3 52.9 + - - +
504A HIS* 2.8 41.4 + - - +
506A ARG 3.3 10.7 - - - +
507A SER* 3.4 8.9 - - - -
508A HIS* 2.8 51.3 + - - +
511A ALA* 3.6 19.4 - - - +
512A VAL* 3.8 18.8 - - - +
38B ALA* 3.7 24.6 - - + +
41B ILE 5.6 0.2 + - - -
42B LEU* 3.7 14.1 + - + +
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Residues in contact with ASN 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497A GLU* 2.9 26.6 + - - +
498A LEU* 3.1 9.9 + - + +
500A GLN* 1.3 76.9 - - - +
502A ILE* 1.3 61.4 + - - +
505A HIS* 2.9 34.2 + - - +
506A ARG* 3.5 26.8 + - - +
507A SER* 3.1 23.8 + - - +
563A PHE* 4.5 10.7 - - + -
565A PRO* 4.2 23.8 - - + +
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Residues in contact with ILE 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498A LEU* 2.9 43.4 + - + +
499A TYR* 3.4 22.4 + - + +
501A ASN* 1.3 77.2 - - - +
503A GLY* 1.3 60.9 + - - +
505A HIS* 4.3 11.4 + - - -
565A PRO* 4.0 23.6 - - + +
568A PHE* 3.9 26.5 - - + +
571A LEU* 4.2 14.1 - - + -
39B ALA* 5.2 4.0 - - + -
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Residues in contact with GLY 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A TYR 2.9 14.5 + - - -
500A GLN 3.9 0.4 - - - -
502A ILE* 1.3 79.8 - - - +
504A HIS* 1.3 65.4 + - - +
505A HIS* 5.4 2.9 + - - -
39B ALA* 3.3 27.6 - - - +
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Residues in contact with HIS 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500A GLN 2.8 19.2 + - - +
503A GLY* 1.3 78.1 + - - +
505A HIS* 1.3 74.0 + - - +
506A ARG* 3.3 18.6 + - + +
38B ALA 2.8 29.5 + - - -
39B ALA 3.3 12.2 + - - -
40B SER 3.8 15.3 - - - -
41B ILE 3.5 3.8 + - - -
42B LEU* 3.7 50.8 + - + +
45B GLU* 4.1 6.3 + - - -
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Residues in contact with HIS 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A ASN* 2.9 30.7 + - - +
502A ILE* 4.3 11.0 + - - -
503A GLY 5.8 2.2 - - - -
504A HIS* 1.3 77.8 + - - +
506A ARG* 1.3 61.2 + - - +
565A PRO* 5.7 6.3 - - + -
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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