Contacts of the helix formed by residues 495 - 506 (chain B) in PDB entry 4L0D
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 495 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410B TRP* 2.7 29.0 + - + -
411B HIS* 3.6 18.6 - - + +
412B LEU 3.2 7.4 - - - -
413B ARG* 4.2 12.3 - - - +
414B VAL* 4.8 1.6 - - - +
490B ILE* 5.5 0.2 - - - +
493B THR 4.0 0.4 + - - -
494B ASP* 1.3 77.4 - - - +
496B LEU* 1.3 64.5 + - - +
497B GLY* 3.3 1.2 + - - +
498B ARG* 3.0 37.1 + - + +
499B LEU* 3.2 8.5 + - - +
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Residues in contact with LEU 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409B TRP* 3.6 34.7 + - + +
412B LEU* 2.8 37.8 + - + +
413B ARG 3.6 16.6 - - - +
414B VAL* 3.9 14.8 - - + -
416B GLU* 5.8 0.2 - - + -
417B LEU* 4.4 11.9 - - + -
495B THR* 1.3 72.5 + - - +
497B GLY* 1.3 56.5 + - - +
499B LEU* 3.1 26.7 - - + +
500B SER* 2.9 28.6 + - - -
539B LEU* 4.4 9.7 - - + +
542B PHE* 4.0 25.8 - - + -
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Residues in contact with GLY 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410B TRP* 3.1 53.2 + - - -
495B THR* 3.1 2.5 + - - -
496B LEU* 1.3 75.3 - - - +
498B ARG* 1.3 58.7 + - - +
500B SER* 2.8 22.7 + - - -
501B HIS* 2.9 17.1 + - - -
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Residues in contact with ARG 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488B LYS* 5.3 10.9 - - - +
490B ILE* 4.4 8.7 - - + -
494B ASP* 5.0 7.0 - - + -
495B THR* 3.0 31.1 + - + +
497B GLY* 1.3 73.3 - - - +
499B LEU* 1.3 58.1 + - - +
501B HIS* 3.2 39.0 + - - +
502B ILE* 2.9 58.2 + - + +
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Residues in contact with LEU 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414B VAL* 5.3 8.5 - - + -
417B LEU* 4.7 4.0 - - + -
490B ILE* 5.0 10.9 - - + +
495B THR 3.2 3.3 + - - +
496B LEU* 3.1 27.8 + - + +
497B GLY 3.0 0.2 - - - -
498B ARG* 1.3 79.5 - - - +
500B SER* 1.3 55.3 + - - +
502B ILE* 3.2 8.0 + - + +
503B LEU* 2.9 57.7 + - + +
509B ALA* 3.8 25.6 - - + -
534B VAL* 4.1 27.4 - - + -
539B LEU* 4.0 26.9 - - + -
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Residues in contact with SER 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ILE 5.0 0.3 - - - +
409B TRP* 3.9 8.0 + - - -
410B TRP* 3.6 28.6 - - - -
496B LEU 2.9 11.6 + - - -
497B GLY 2.8 15.2 + - - -
499B LEU* 1.3 71.2 - - - +
501B HIS* 1.3 57.2 + - - -
503B LEU* 3.3 11.0 + - - +
504B GLU* 2.9 35.1 + - - +
539B LEU* 3.8 16.2 - - - +
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Residues in contact with HIS 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A ARG* 5.2 8.1 + - - +
410B TRP* 3.7 29.0 + + - -
497B GLY 2.9 14.3 + - - -
498B ARG* 3.4 32.3 - - - +
500B SER* 1.3 75.1 - - - +
502B ILE* 1.3 58.1 + - - +
504B GLU* 2.7 49.3 + - - +
505B MET* 3.0 7.8 + - - +
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Residues in contact with ILE 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488B LYS* 3.6 35.9 - - + +
489B GLN 4.2 6.7 - - - +
490B ILE* 3.6 36.8 - - + -
498B ARG* 2.9 42.9 + - + +
499B LEU* 3.6 6.3 - - + +
501B HIS* 1.3 75.5 - - - +
503B LEU* 1.3 52.7 + - + +
505B MET* 2.7 9.6 + - + +
506B ASP* 2.5 41.1 + - + +
509B ALA* 4.6 12.8 - - + -
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Residues in contact with LEU 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A ILE 3.6 8.2 - - - +
189A VAL* 3.9 1.8 - - + +
190A ARG 3.6 18.0 + - - -
499B LEU* 2.9 52.6 + - + +
500B SER* 3.6 6.7 - - - +
502B ILE* 1.3 74.3 - - + +
504B GLU* 1.3 64.5 + - - +
506B ASP 3.3 22.6 - - - +
507B HIS 4.1 13.5 - - - +
509B ALA* 4.6 6.7 - - + +
534B VAL 4.4 4.5 - - - +
535B THR 3.9 7.9 - - - +
536B ALA* 3.7 38.1 - - + +
539B LEU* 4.1 15.0 - - + -
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Residues in contact with GLU 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A VAL* 4.8 4.4 - - + +
182A ARG* 2.7 47.6 + - - +
186A ALA 5.0 3.3 - - - +
187A GLU* 5.3 1.4 - - - -
188A ILE* 3.8 44.2 + - + +
190A ARG* 3.1 26.9 + - - +
410B TRP* 6.1 0.7 - - - -
500B SER* 2.9 21.7 + - - +
501B HIS* 2.7 26.4 + - - +
503B LEU* 1.3 78.9 - - - +
505B MET* 1.3 59.1 + - + +
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Residues in contact with MET 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A GLU* 4.6 2.3 - - - +
175A SER* 3.8 31.0 - - - -
178A VAL* 4.7 14.1 - - + -
182A ARG* 5.5 7.2 - - - +
190A ARG* 4.0 26.9 + - - +
486B GLN* 3.6 9.2 + - - -
501B HIS 3.0 8.7 + - - +
502B ILE* 2.7 11.1 + - + +
504B GLU* 1.3 82.6 - - + +
506B ASP* 1.3 71.0 + - - +
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Residues in contact with ASP 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A GLU* 3.9 3.2 - - - +
190A ARG* 4.1 7.1 + - - +
486B GLN* 2.7 42.6 + - - +
487B PHE* 4.2 8.1 + - - +
488B LYS* 3.4 26.1 - - - +
502B ILE* 2.5 23.9 + - + +
503B LEU* 3.3 27.9 + - - +
504B GLU 3.6 1.6 - - - -
505B MET* 1.3 83.4 - - - +
507B HIS* 1.3 64.3 + - - +
508B PHE 4.1 13.9 - - - +
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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