Contacts of the helix formed by residues 447 - 454 (chain A) in PDB entry 1SL1
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 TYR 447 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242A LEU* 3.9 15.5 - - + -
245A GLU* 3.5 25.6 + - - +
246A LEU* 3.7 27.2 - - + +
249A ARG* 4.7 7.8 - - - +
388A GLU* 5.0 3.5 + - - -
391A MET* 3.9 28.9 - - + -
392A ILE* 4.3 14.5 - - + +
395A ARG* 4.3 12.8 - - + +
445A SER 3.1 1.2 + - - -
446A PRO* 1.3 80.0 - - + +
448A GLY* 1.3 63.9 + - - +
449A GLU* 3.3 3.4 - - - -
450A GLN* 3.3 26.0 + - - +
451A CYS* 3.0 27.9 + - - -
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Residues in contact with GLY 448 (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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441A PRO* 3.9 15.0 - - - -
442A GLY 3.0 28.5 - - - -
443A VAL* 3.9 2.0 - - - -
445A SER 2.8 9.4 + - - -
446A PRO 3.0 2.8 + - - -
447A TYR* 1.3 78.6 - - - +
449A GLU* 1.3 55.2 + - - +
451A CYS* 3.2 0.7 + - - +
452A ARG* 2.8 35.9 + - - +
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Residues in contact with GLU 449 (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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443A VAL* 3.9 26.4 + - + +
447A TYR* 3.3 1.4 - - - +
448A GLY* 1.3 75.2 - - - +
450A GLN* 1.3 59.7 + - + +
453A ALA* 3.0 33.2 + - + +
701A ALA* 3.7 13.4 - - + +
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Residues in contact with GLN 450 (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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238A ALA* 5.6 2.0 + - - +
239A ILE* 4.3 5.1 - - + +
242A LEU* 3.5 32.4 - - + +
245A GLU* 3.8 14.7 + - - +
447A TYR* 3.3 32.2 + - - +
448A GLY 3.3 0.6 - - - -
449A GLU* 1.3 78.7 - - + +
451A CYS* 1.3 67.1 + - - +
453A ALA* 3.6 4.9 + - - +
454A ALA* 3.3 20.6 + - - +
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Residues in contact with CYS 451 (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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239A ILE* 4.6 3.8 - - - +
242A LEU* 4.2 15.5 - - - -
395A ARG* 4.4 11.4 - - - -
399A SER* 5.7 1.1 - - - -
406A TRP* 3.6 36.6 - - + -
440A ILE* 4.2 10.5 - - + -
441A PRO* 4.1 17.7 - - + -
447A TYR 3.0 23.1 + - - +
448A GLY 3.6 7.6 - - - +
450A GLN* 1.3 77.8 - - - +
452A ARG* 1.3 61.4 + - - +
454A ALA* 3.2 17.8 + - - +
455A PHE* 3.4 13.9 - - - -
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Residues in contact with ARG 452 (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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440A ILE* 2.7 49.3 + - - +
441A PRO 2.9 25.3 + - - +
442A GLY* 3.7 9.2 - - - -
443A VAL* 4.1 14.3 - - + +
448A GLY 2.8 14.8 + - - +
451A CYS* 1.3 72.0 - - - +
453A ALA* 1.3 63.9 + - - +
454A ALA 3.1 2.5 - - - -
455A PHE* 3.1 24.0 + - - +
655A GLU* 4.6 0.8 + - - -
700A TRP* 3.4 56.7 + - - +
701A ALA* 3.6 23.9 + - + +
704A HIS* 4.0 15.9 + - - -
20P C 4.3 3.2 + - - -
21P T 3.9 20.4 + - - -
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Residues in contact with ALA 453 (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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449A GLU* 3.0 21.3 + - + +
450A GLN* 4.1 5.4 - - - +
451A CYS 3.4 0.2 - - - -
452A ARG* 1.3 77.0 - - - +
454A ALA* 1.3 51.4 + - - +
455A PHE 3.2 0.6 + - - -
458A GLU* 4.0 0.2 - - - +
459A HIS* 2.7 29.5 + - - -
699A ASN* 3.5 35.9 + - - +
701A ALA* 3.6 5.8 - - + +
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Residues in contact with ALA 454 (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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234A PHE* 3.4 10.0 - - + -
235A ASP* 2.8 38.0 + - + -
238A ALA* 5.1 4.3 - - + -
239A ILE* 3.5 35.7 - - + -
450A GLN 3.3 7.0 + - - +
451A CYS 3.2 14.3 + - - +
452A ARG 3.1 0.8 - - - -
453A ALA* 1.3 78.4 - - - +
455A PHE* 1.3 56.8 - - - +
459A HIS* 3.1 10.3 - - - -
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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