Contacts of the helix formed by residues 408 - 415 (chain A) in PDB entry 4H1S
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 TRP 408 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A TYR* 3.2 47.4 + + + +
337A GLN* 3.9 6.8 + - + +
339A LEU* 3.8 31.7 - - + +
407A THR* 1.3 74.8 - - - +
409A GLU* 1.3 57.5 + - - +
411A LEU* 3.3 2.3 + - + +
412A ALA* 2.9 31.9 + - + +
525A ILE* 4.0 31.9 - - + +
526A ASN* 3.4 25.8 - - - -
529A SER* 3.3 27.4 - - - -
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Residues in contact with GLU 409 (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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42A GLU* 4.7 0.3 - - - +
50A LYS* 3.0 34.1 + - + +
90A THR* 6.3 1.1 - - - -
91A ILE* 3.6 30.6 + - + +
328A ARG* 2.9 44.6 + - - -
334A TYR* 3.6 22.0 + - + +
407A THR* 3.2 8.9 + - - +
408A TRP* 1.3 76.2 - - - +
410A ASN* 1.3 66.9 + - - +
411A LEU 3.3 0.7 + - - -
412A ALA* 3.4 2.8 + - - +
413A ALA* 3.4 19.6 + - - +
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Residues in contact with ASN 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A SER* 6.3 0.4 - - - -
50A LYS* 4.2 30.1 - - - +
397A PRO 5.2 0.7 - - - +
398A ILE* 3.8 31.5 - - + +
402A ASN* 5.6 2.0 + - - -
405A THR 3.7 7.8 - - - +
406A ILE* 3.7 8.6 - - + -
407A THR* 3.0 35.1 + - - +
409A GLU* 1.3 77.6 - - - +
411A LEU* 1.3 63.0 + - - +
413A ALA* 3.4 13.2 + - - +
414A VAL* 3.4 16.5 - - - +
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Residues in contact with LEU 411 (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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339A LEU* 3.8 9.9 - - + -
360A MET* 6.0 2.7 - - - -
363A LEU* 6.3 0.7 - - + -
398A ILE* 4.3 13.9 - - + -
406A ILE* 4.9 1.8 - - + -
407A THR 3.2 11.8 + - - +
408A TRP* 3.8 5.4 - - + +
409A GLU 3.2 0.8 - - - -
410A ASN* 1.3 74.9 - - - +
412A ALA* 1.3 61.9 + - - +
413A ALA 3.1 1.8 - - - -
414A VAL* 2.9 31.3 + - + +
415A LEU* 3.0 18.4 + - + +
525A ILE* 4.0 20.0 - - + +
528A VAL* 3.9 22.9 - - + -
529A SER* 3.6 42.0 - - - +
532A ILE* 4.5 10.8 - - + -
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Residues in contact with ALA 412 (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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89A GLY 4.7 1.4 - - - +
90A THR* 5.1 3.1 - - - -
91A ILE* 3.8 22.7 - - + +
94A THR* 4.8 10.0 + - + +
334A TYR* 5.6 0.4 - - + -
408A TRP* 2.9 23.3 + - + +
409A GLU 3.8 4.5 - - - +
411A LEU* 1.3 77.8 - - - +
413A ALA* 1.3 57.0 + - - +
415A LEU 4.0 2.9 - - - +
416A PRO* 3.3 28.2 - - + +
525A ILE* 3.6 18.7 - - + +
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Residues in contact with ALA 413 (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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40A ARG* 5.5 1.3 - - - +
49A SER* 6.5 0.7 - - - -
89A GLY 3.5 24.8 - - - +
90A THR* 4.6 10.9 - - + +
395A ARG* 3.3 20.1 - - - +
396A SER* 3.4 22.3 - - - +
409A GLU 3.4 10.3 + - - +
410A ASN* 3.6 11.4 - - - +
411A LEU 3.1 0.8 - - - -
412A ALA* 1.3 76.6 - - - +
414A VAL* 1.3 63.1 + - - +
416A PRO* 4.2 1.3 - - - +
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Residues in contact with VAL 414 (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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360A MET* 3.7 37.5 - - + -
364A ILE* 4.2 5.2 - - + -
393A GLY 3.5 1.4 - - - +
394A ILE* 4.1 9.4 - - + -
395A ARG 2.9 21.5 + - - -
396A SER* 3.5 29.6 - - - +
398A ILE* 3.7 13.7 - - + -
410A ASN 3.4 17.7 - - - +
411A LEU* 2.9 13.7 + - + +
413A ALA* 1.3 77.7 - - - +
415A LEU* 1.3 77.8 + - + +
416A PRO* 3.5 4.9 - - - +
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Residues in contact with LEU 415 (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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364A ILE* 4.0 25.1 - - + -
389A LEU* 5.8 3.8 - - + -
393A GLY 3.8 14.8 - - - +
394A ILE* 5.4 0.7 - - + -
411A LEU* 3.0 14.6 + - + +
412A ALA* 3.5 6.0 - - - +
414A VAL* 1.3 94.8 - - + +
416A PRO* 1.3 62.0 - - - +
417A PHE* 3.5 4.4 + - + -
418A GLY 4.8 0.7 + - - -
421A PHE* 4.5 10.3 - - + -
524A ASP* 4.2 24.7 - - + +
525A ILE* 4.0 28.7 - - + +
528A VAL* 3.7 35.0 - - + -
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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