Contacts of the helix formed by residues 493 - 505 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A VAL* 4.3 6.9 - - - +
34A VAL 4.8 2.2 + - - -
53A LEU* 4.1 18.4 - - - +
54A THR 5.5 0.4 + - - -
438B PHE* 4.5 2.7 - - - -
464B GLY* 3.3 18.5 - - - -
492B THR* 1.3 72.7 - - - +
494B GLY* 1.3 62.8 + - - +
495B LEU 3.5 2.0 - - - -
496B ILE* 3.2 16.7 + - + +
497B GLU 3.2 15.9 + - - -
511B ALA 4.9 1.8 + - - -
512B VAL* 3.0 19.7 + - + +
514B PHE* 3.2 29.5 - - - -
600B TP9 3.4 38.5 - - + +
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Residues in contact with GLY 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412B PHE* 4.7 3.8 - - - -
490B ASN* 4.5 8.3 - - - -
492B THR* 3.1 14.1 + - - -
493B ASN* 1.3 69.9 - - - +
495B LEU* 1.3 64.9 + - - +
497B GLU* 3.1 7.6 + - - +
498B LEU* 3.1 19.4 + - - +
561B TYR* 4.5 7.0 - - - -
600B TP9 2.8 25.9 + - - -
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Residues in contact with LEU 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B TYR* 3.8 39.9 - - + +
410B ILE* 5.5 2.2 - - + -
411B GLY* 4.0 17.7 - - - +
412B PHE* 3.6 37.3 - - + +
415B HIS* 4.9 6.1 - - + +
493B ASN 3.5 0.2 - - - -
494B GLY* 1.3 71.7 - - - +
496B ILE* 1.3 59.6 + - + +
498B LEU* 3.1 13.6 + - + +
499B TYR* 2.9 45.9 + - + -
600B TP9 2.8 32.4 + - - +
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Residues in contact with ILE 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A VAL* 3.4 27.8 - - + +
35A GLY* 3.5 39.0 - - - +
36A ARG* 3.9 5.4 - - + +
38A ALA* 3.7 10.3 - - + -
493B ASN* 3.5 14.8 - - + +
494B GLY 3.1 0.8 - - - -
495B LEU* 1.3 79.9 - - + +
497B GLU* 1.3 60.0 + - - +
499B TYR* 3.3 8.3 + - + +
500B GLN* 2.9 26.7 + - - +
511B ALA 4.9 0.4 - - - +
512B VAL* 3.7 17.7 - - + -
600B TP9 3.8 36.1 - - + +
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Residues in contact with GLU 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490B ASN* 5.6 1.4 + - - -
492B THR* 3.5 7.8 - - + +
493B ASN 3.2 10.3 + - - +
494B GLY* 3.1 10.0 + - - +
496B ILE* 1.3 72.7 - - - +
498B LEU* 1.3 64.1 + - - +
500B GLN* 3.3 12.3 + - - +
501B ASN* 2.8 34.4 + - - +
507B SER* 2.9 33.3 + - - +
509B ASP* 4.8 0.7 - - - +
512B VAL* 3.8 11.3 - - + +
513B LYS* 3.2 34.6 + - - -
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Residues in contact with LEU 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B TYR* 4.6 9.4 - - + -
412B PHE* 3.9 37.0 - - + -
494B GLY 3.1 11.3 + - - +
495B LEU* 3.1 19.3 + - + +
497B GLU* 1.3 76.1 - - - +
499B TYR* 1.3 58.5 + - + +
501B ASN* 3.2 10.1 + - + +
502B ILE* 2.9 54.2 + - + +
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Residues in contact with TYR 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ARG* 3.7 60.6 - - + +
38A ALA* 4.3 3.6 - - + -
39A ALA* 3.4 24.4 - - + +
271B TYR* 2.4 37.8 + + - -
495B LEU* 2.9 44.9 + - + -
496B ILE* 3.3 10.7 + - + +
498B LEU* 1.3 77.1 - - + +
500B GLN* 1.3 62.3 + - - +
502B ILE* 3.4 20.9 + - + +
503B GLY 3.1 19.1 + - - -
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Residues in contact with GLN 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ALA* 3.8 24.5 - - + +
41A ILE 5.4 0.2 + - - -
42A LEU* 3.8 14.6 + - + +
496B ILE* 2.9 17.9 + - - +
497B GLU* 3.4 8.9 - - - +
499B TYR* 1.3 74.2 - - - +
501B ASN* 1.3 57.6 + - - +
504B HIS* 2.8 31.2 + - - +
506B ARG 3.3 17.5 - - - +
507B SER* 3.4 8.4 - - - -
508B HIS* 2.8 50.5 + - - +
511B ALA* 3.5 20.0 - - - +
512B VAL* 3.7 20.2 - - + +
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Residues in contact with ASN 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497B GLU* 2.8 29.1 + - - +
498B LEU* 3.6 11.6 - - + +
500B GLN* 1.3 79.0 - - - +
502B ILE* 1.3 61.1 + - - +
505B HIS* 2.9 32.9 + - - -
506B ARG* 3.4 28.2 + - - +
507B SER* 3.2 21.8 + - - +
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Residues in contact with ILE 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ALA* 5.4 3.6 - - + -
271B TYR* 6.0 2.2 - - + -
498B LEU* 2.9 49.4 + - + +
499B TYR* 3.4 27.1 + - + +
501B ASN* 1.3 78.9 - - - +
503B GLY* 1.3 59.9 + - - +
505B HIS* 4.1 13.1 + - - -
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Residues in contact with GLY 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ALA* 3.4 26.7 - - - +
499B TYR 3.1 12.8 + - - -
500B GLN 4.0 0.2 - - - -
502B ILE* 1.3 78.0 - - - +
504B HIS* 1.3 68.4 + - - +
505B HIS* 3.9 2.3 - - - -
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Residues in contact with HIS 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ALA 2.9 29.2 + - - -
39A ALA 3.2 15.5 + - - -
40A SER* 3.9 12.1 - - - -
41A ILE 3.5 5.5 + - - -
42A LEU* 3.5 47.5 - - + +
45A GLU* 4.1 7.2 + - - -
500B GLN 2.8 17.1 + - - +
503B GLY* 1.3 82.4 + - - +
505B HIS* 1.3 74.1 + - - +
506B ARG* 3.4 17.3 + - + +
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Residues in contact with HIS 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501B ASN* 2.9 30.5 + - - +
502B ILE* 4.1 11.7 + - - -
503B GLY 5.4 1.3 - - - -
504B HIS* 1.3 79.7 + - - +
506B ARG* 1.3 63.8 + - - +
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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