Contacts of the helix formed by residues 377 - 387 (chain I) in PDB entry 6ALH
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 377 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364I VAL* 6.0 3.0 - - - +
367I TYR* 4.1 7.7 + - - -
375I PRO* 3.5 11.4 + - - +
376I PRO* 1.3 77.8 + - - +
378I ARG* 1.3 72.3 + - - +
379I GLU* 4.4 6.5 - - + +
380I ALA* 3.8 24.9 - - + +
381I ALA* 3.1 22.5 + - - +
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Residues in contact with ARG 378 (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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359I ARG* 5.3 6.4 - - - +
360I LEU* 3.4 57.0 - - + +
363I LEU* 4.6 3.3 - - - +
364I VAL* 6.4 0.2 - - - -
377I THR* 1.3 78.1 - - - +
379I GLU* 1.3 81.0 + - - +
381I ALA* 3.1 3.6 + - - +
382I GLU* 2.9 51.2 + - + +
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Residues in contact with GLU 379 (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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377I THR* 4.4 6.0 - - + +
378I ARG* 1.3 102.9 + - - +
380I ALA* 1.3 60.7 + - - +
382I GLU* 3.3 23.1 - - - +
383I SER* 2.9 34.6 + - - +
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Residues in contact with ALA 380 (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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367I TYR* 4.4 20.3 - - + +
377I THR* 3.8 27.4 + - + +
378I ARG 3.2 0.8 - - - -
379I GLU* 1.3 77.7 - - - +
381I ALA* 1.3 56.9 + - - +
383I SER* 3.5 5.6 + - - -
384I LEU* 2.9 28.5 + - - +
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Residues in contact with ALA 381 (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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363I LEU* 3.4 47.3 - - + +
364I VAL* 5.4 0.9 - - + -
367I TYR* 3.7 16.5 - - + -
376I PRO* 6.5 0.2 - - + -
377I THR 3.1 17.4 + - - +
378I ARG* 3.1 5.8 + - - +
380I ALA* 1.3 72.6 - - - +
382I GLU* 1.3 60.3 + - - +
384I LEU* 3.4 8.9 - - + +
385I PHE* 2.9 24.9 + - - +
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Residues in contact with GLU 382 (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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359I ARG* 4.7 11.7 + - - +
363I LEU* 3.7 21.3 - - + -
378I ARG* 2.9 50.6 + - + +
379I GLU* 3.3 32.1 - - - +
380I ALA 3.3 0.2 - - - -
381I ALA* 1.3 76.7 - - - +
383I SER* 1.3 57.5 + - - +
385I PHE* 3.9 0.7 - - - +
386I GLU* 3.0 37.8 + - + +
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Residues in contact with SER 383 (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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379I GLU* 2.9 18.1 + - - +
380I ALA* 3.9 4.9 - - - -
382I GLU* 1.3 75.4 - - - +
384I LEU* 1.3 56.6 + - - +
386I GLU* 3.7 4.0 - - - -
387I ASN* 2.9 46.6 + - - +
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Residues in contact with LEU 384 (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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366I ILE* 4.8 3.8 - - + -
367I TYR* 3.6 37.0 - - + +
370I MET* 3.8 30.7 - - + -
371I ARG* 6.6 0.2 - - - -
380I ALA 2.9 18.8 + - - +
381I ALA* 3.4 7.0 - - - +
383I SER* 1.3 76.0 - - - +
385I PHE* 1.3 58.9 + - + +
387I ASN* 2.9 7.3 + - - -
388I LEU* 2.9 54.3 + - + +
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Residues in contact with PHE 385 (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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198I ILE* 5.5 0.9 - - + -
209I ILE* 4.5 18.6 - - + -
212I ALA* 3.9 24.9 - - + -
213I LEU* 3.9 25.1 - - + -
359I ARG* 5.9 3.6 - - - -
363I LEU* 3.7 19.5 - - + -
366I ILE* 4.1 33.2 - - + -
381I ALA 2.9 18.3 + - - +
382I GLU 4.5 0.7 - - - +
384I LEU* 1.3 75.2 - - + +
386I GLU* 1.3 65.9 + - + +
387I ASN 3.5 0.2 + - - -
388I LEU* 3.9 11.8 + - + +
389I PHE* 4.1 26.3 + + - -
390I PHE* 4.0 24.2 - + - -
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Residues in contact with GLU 386 (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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359I ARG* 4.0 20.8 + - - +
382I GLU* 3.0 24.5 + - + +
383I SER* 4.0 4.9 - - - +
385I PHE* 1.3 82.9 - - + +
387I ASN* 1.3 67.2 + - - +
388I LEU 3.6 0.2 - - - -
390I PHE* 3.4 44.3 - - - +
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Residues in contact with ASN 387 (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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383I SER* 2.9 30.3 + - - +
384I LEU* 2.9 7.9 + - - +
386I GLU* 1.3 88.1 - - - +
388I LEU* 1.3 59.8 + - - +
389I PHE 3.6 0.4 - - - -
390I PHE 4.8 0.7 - - - -
391I SER* 3.4 25.0 + - - -
393I ASP* 5.5 1.7 - - + +
394I ARG* 3.7 44.4 + - - +
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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