Contacts of the helix formed by residues 370 - 379 (chain I) in PDB entry 5IIO
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 THR 370 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343I GLY* 5.7 0.2 - - - -
368I SER 4.3 0.6 + - - +
369I LEU* 1.3 77.8 - - - +
371I THR* 1.3 66.0 + - - +
372I GLN* 3.5 9.6 + - - +
373I GLN* 2.9 50.2 + - - +
374I ALA* 3.0 19.4 + - - +
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Residues in contact with THR 371 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370I THR* 1.3 74.6 - - - +
372I GLN* 1.3 65.1 + - + +
374I ALA* 3.5 8.2 - - + +
375I ILE* 3.4 31.4 + - + +
460I ASP 5.8 1.1 - - - +
11J G 4.8 9.3 + - - -
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Residues in contact with GLN 372 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342I TRP* 3.6 33.7 - - + +
343I GLY* 4.9 6.4 - - - -
370I THR* 3.2 8.1 + - - +
371I THR* 1.3 78.8 - - - +
373I GLN* 1.3 59.6 + - - +
375I ILE* 3.2 8.1 + - + +
376I GLY 2.9 23.2 + - - -
461I LEU* 2.8 40.5 + - + +
462I VAL* 3.3 19.2 - - - +
10J T 5.4 12.6 - - - +
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Residues in contact with GLN 373 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341I ILE* 3.5 6.5 - - + +
342I TRP 3.6 7.4 - - - -
343I GLY* 3.1 37.8 + - - -
344I ALA* 3.9 5.6 - - + +
348I THR* 3.9 21.5 + - - +
352I TRP* 4.0 14.4 - - + -
368I SER 4.2 1.4 - - - +
369I LEU* 3.6 20.5 - - + +
370I THR* 2.9 45.5 + - - +
372I GLN* 1.3 72.8 - - - +
374I ALA* 1.3 56.4 + - - +
377I LEU* 2.7 36.9 + - - +
4K T 5.3 0.8 - - - -
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Residues in contact with ALA 374 (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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369I LEU* 4.2 20.3 - - + +
370I THR 3.0 12.7 + - - +
371I THR* 3.5 14.1 - - - +
373I GLN* 1.3 76.9 - - - +
375I ILE* 1.3 63.6 + - + +
377I LEU* 3.4 2.4 + - - +
378I LYS* 3.0 27.2 + - - +
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Residues in contact with ILE 375 (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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371I THR* 3.4 24.8 + - + +
372I GLN* 3.2 8.1 + - + +
374I ALA* 1.3 78.0 - - + +
376I GLY* 1.3 63.6 + - - +
378I LYS* 3.3 8.5 + - + +
379I HIS* 3.1 38.0 + - + +
383I PHE* 4.7 2.0 - - + -
459I ASP* 3.8 34.8 - - + +
460I ASP 3.3 29.4 - - - +
461I LEU* 3.7 19.1 - - + -
476I VAL* 4.0 6.7 - - + -
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Residues in contact with GLY 376 (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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340I ASN 5.5 0.3 - - - +
341I ILE* 3.8 8.7 - - - +
342I TRP* 3.9 28.4 + - - -
372I GLN 2.9 14.8 + - - -
373I GLN 3.2 3.3 + - - -
375I ILE* 1.3 76.8 - - - +
377I LEU* 1.3 60.3 + - - +
379I HIS 3.6 2.4 + - - +
380I TYR* 3.2 22.5 + - - +
383I PHE* 4.4 11.1 - - - +
461I LEU* 4.7 0.6 - - - +
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Residues in contact with LEU 377 (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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341I ILE* 3.6 18.0 - - + +
360I LEU* 4.0 33.7 - - + +
363I ILE* 3.9 7.2 - - + -
364I ARG* 3.7 60.1 + - + +
369I LEU* 3.7 23.6 - - + -
373I GLN 2.7 20.6 + - - +
374I ALA* 3.9 3.4 - - - +
376I GLY* 1.3 70.3 - - - +
378I LYS* 1.3 65.9 + - - +
380I TYR* 3.1 22.0 + - + +
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Residues in contact with LYS 378 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364I ARG* 5.8 3.1 - - - +
374I ALA 3.0 16.2 + - - +
375I ILE* 3.7 7.6 - - + +
377I LEU* 1.3 78.4 - - - +
379I HIS* 1.3 95.2 + - + +
380I TYR 3.3 1.0 + - - -
459I ASP* 4.6 10.3 - - - +
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Residues in contact with HIS 379 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375I ILE* 3.1 32.9 + - + +
376I GLY 3.6 3.8 - - - -
378I LYS* 1.3 97.2 + - + +
380I TYR* 1.3 64.0 + - - +
381I SER 3.4 2.0 - - - -
382I ASP* 3.3 12.9 + - + -
383I PHE* 3.0 52.1 + + + -
459I ASP* 2.7 28.5 + - - -
476I VAL* 4.2 3.8 - - + -
486I HIS* 3.4 46.3 + + + +
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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