Contacts of the helix formed by residues 398 - 403 (chain I) in PDB entry 1I43
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 GLN 398 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370I LEU* 3.6 22.4 + - - +
373I THR* 3.3 26.1 - - + +
374I ALA* 3.4 23.7 - - - +
377I VAL* 4.1 7.3 - - + +
397I ASP* 1.3 75.2 - - - +
399I PRO* 1.3 54.1 - - - -
400I ALA* 2.6 7.2 + - + +
401I ILE* 2.6 50.7 + - + +
402I MET* 2.9 13.2 + - - +
419I ASP 3.3 23.0 + - - +
421I LEU 3.4 16.6 - - - +
422I VAL* 4.2 4.0 - - + -
92K THR* 4.0 7.4 + - - +
95K LEU* 5.5 3.9 - - + +
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Residues in contact with PRO 399 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212I PRO* 4.6 11.9 - - + -
397I ASP* 3.1 27.8 - - - +
398I GLN* 1.3 82.2 - - - -
400I ALA* 1.3 61.6 + - - +
402I MET* 4.3 0.4 - - + -
403I SER* 3.0 29.1 + - - +
404I TYR* 3.1 24.6 + - + -
417I ILE* 4.0 11.2 - - + -
421I LEU* 3.8 31.0 - - + +
423I ARG* 4.0 18.6 - - + +
608I PMC 5.8 1.3 - - - +
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Residues in contact with ALA 400 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370I LEU* 4.8 2.7 - - + -
398I GLN* 2.6 9.2 + - + +
399I PRO* 1.3 76.8 - - - +
401I ILE* 1.3 62.7 + - + +
404I TYR* 3.1 6.8 - - - +
405I TRP* 3.1 29.6 + - - -
412I ARG* 3.8 10.9 - - - +
417I ILE* 3.6 15.7 - - + +
418I MET 3.6 23.5 + - - +
419I ASP* 4.1 20.4 - - - +
421I LEU 5.2 0.4 + - - -
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Residues in contact with ILE 401 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370I LEU* 3.8 28.0 - - + -
374I ALA* 5.2 0.2 - - + -
398I GLN* 2.6 27.6 + - + +
400I ALA* 1.3 73.0 - - - +
402I MET* 1.3 64.0 + - - +
403I SER 3.6 0.2 + - - -
405I TRP* 3.2 47.0 - - + +
92K THR* 3.6 28.9 - - + -
95K LEU* 3.8 25.8 - - + -
96K ILE* 3.9 21.8 - - + -
99K LYS* 3.7 12.6 - - + -
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Residues in contact with MET 402 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385I ILE 4.8 0.4 - - - -
386I ALA* 3.6 8.5 - - - +
387I PRO* 3.4 45.5 - - + -
397I ASP* 3.2 35.9 - - + +
398I GLN 2.9 10.7 + - - +
401I ILE* 1.3 78.8 - - - +
403I SER* 1.3 59.4 + - - +
608I PMC 3.4 9.4 + - - +
89K PHE* 3.5 28.0 - - + -
95K LEU* 4.0 23.6 - - + -
99K LYS* 2.6 29.8 + - - +
107K GLU* 4.3 10.8 - - + +
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Residues in contact with SER 403 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164I ARG* 3.0 30.1 + - - -
399I PRO* 3.0 12.9 + - - +
402I MET* 1.3 79.1 - - - +
404I TYR* 1.3 79.3 - - - +
405I TRP 3.8 1.1 - - - -
406I ASP* 4.5 0.9 - - - -
608I PMC 2.8 49.0 + - - -
99K LYS* 4.6 3.1 - - - +
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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