Contacts of the helix formed by residues 554 - 562 (chain B) in PDB entry 1IGN
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 ILE 554 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458B ALA* 3.5 29.4 - - - +
461B VAL* 3.5 31.6 - - + -
462B LYS* 4.5 3.1 - - + -
465B PHE* 4.0 18.2 - - + -
515B GLN* 4.1 21.3 - - + +
517B ARG 5.2 1.3 - - - +
545B PHE* 4.3 9.6 - - + -
549B LEU* 3.8 24.7 - - + +
550B LEU* 4.5 11.0 - - + +
553B GLY* 1.3 71.6 - - - +
555B ASP* 1.3 64.2 + - - +
557B TYR* 3.7 1.9 + - - +
558B ILE* 3.1 31.4 + - + +
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Residues in contact with ASP 555 (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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462B LYS* 5.0 2.9 + - - +
513B ARG 4.4 1.2 - - - +
514B THR* 3.1 29.9 + - + +
515B GLN* 2.7 60.1 + - - +
553B GLY* 5.5 0.2 - - - -
554B ILE* 1.3 74.7 + - - +
556B ASP* 1.3 75.2 + - - +
558B ILE* 3.0 10.5 + - - +
559B SER* 2.9 26.5 + - - -
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Residues in contact with ASP 556 (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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552B TYR* 3.3 34.5 + - + +
553B GLY* 3.3 17.7 - - - +
554B ILE 4.1 0.2 + - - -
555B ASP* 1.3 82.3 + - - +
557B TYR* 1.3 57.0 + - - +
559B SER* 2.8 20.8 + - - -
560B TYR* 3.0 16.6 + - - +
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Residues in contact with TYR 557 (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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451B ALA* 3.2 27.0 - - - +
454B ASP* 3.9 11.4 - - + -
455B TYR* 3.6 30.7 - - - -
458B ALA* 4.5 4.9 - - + -
549B LEU* 4.7 9.2 - - + -
552B TYR* 3.5 20.6 - + + -
553B GLY 3.1 9.5 + - - +
554B ILE 4.2 2.9 - - - +
556B ASP* 1.3 77.2 - - - +
558B ILE* 1.3 62.8 + - - +
560B TYR* 3.7 17.9 - + - -
561B TYR* 2.8 46.8 + - + +
572B GLU 2.9 28.4 + - - -
573B PRO* 3.8 1.3 - - - +
574B MET* 3.6 31.9 - - + -
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Residues in contact with ILE 558 (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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455B TYR* 4.0 17.0 - - + -
458B ALA* 3.7 28.0 - - + +
459B ILE* 3.7 21.3 - - + -
462B LYS* 3.8 34.1 - - + +
554B ILE* 3.1 25.2 + - + +
555B ASP* 3.0 8.5 + - - +
557B TYR* 1.3 76.5 - - - +
559B SER* 1.3 59.3 + - - +
562B GLU* 3.0 54.3 + - - +
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Residues in contact with SER 559 (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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555B ASP 2.9 12.4 + - - -
556B ASP* 2.8 21.1 + - - -
558B ILE* 1.3 75.6 - - - +
560B TYR* 1.3 55.4 + - - +
562B GLU* 3.6 4.9 - - - +
563B ALA* 2.7 38.5 + - - +
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Residues in contact with TYR 560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552B TYR* 3.9 20.6 - + - +
556B ASP 3.0 15.0 + - - +
557B TYR* 3.6 23.6 - + - +
559B SER* 1.3 84.8 + - - +
561B TYR* 1.3 81.4 + - - +
563B ALA* 3.0 17.8 + - + +
564B GLU* 3.6 28.5 + - + +
572B GLU* 3.4 53.9 + - - +
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Residues in contact with TYR 561 (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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451B ALA* 3.7 26.7 - - + -
452B ASP* 2.9 30.9 + - - -
455B TYR* 3.5 53.7 - + + -
557B TYR* 2.8 40.3 + - + +
560B TYR* 1.3 82.8 - - + +
562B GLU* 1.3 68.2 + - + +
563B ALA 3.3 0.3 + - - -
564B GLU* 3.4 18.4 + - - +
572B GLU* 4.1 11.6 - - - +
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Residues in contact with GLU 562 (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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455B TYR* 2.9 32.6 + - + +
459B ILE* 4.7 2.4 - - - +
558B ILE* 3.0 37.3 + - - +
559B SER* 3.9 4.7 - - - +
561B TYR* 1.3 78.8 - - + +
563B ALA* 1.3 64.9 + - - +
564B GLU 3.3 5.8 + - - +
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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