Contacts of the helix formed by residues 405 - 415 (chain D) in PDB entry 5E9W
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 ASN 405 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401D GLU 4.4 1.5 + - - +
402D LYS* 3.2 5.5 + - - +
403D ILE 2.9 1.3 - - - -
404D LYS* 1.3 80.5 - - - +
406D ASN* 1.3 57.6 + - - +
407D GLU* 2.7 27.4 + - - +
408D ASN* 2.9 49.8 + - - +
409D LYS* 2.9 29.1 + - - +
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Residues in contact with ASN 406 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404D LYS 4.1 1.8 + - - -
405D ASN* 1.3 72.0 + - - +
407D GLU* 1.3 71.9 + - - +
409D LYS* 3.5 24.3 - - - +
410D MET* 3.0 47.3 + - - +
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Residues in contact with GLU 407 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405D ASN* 2.7 24.3 + - - +
406D ASN* 1.3 81.3 + - - +
408D ASN* 1.3 60.8 + - - +
409D LYS 3.1 0.2 - - - -
410D MET* 3.3 2.7 + - - +
411D LEU* 2.8 30.8 + - - +
414D ARG* 3.9 11.0 + - - +
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Residues in contact with ASN 408 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178D TRP* 2.7 37.8 + - + +
182D VAL* 3.9 30.9 - - + +
402D LYS* 3.4 29.0 + - - +
405D ASN* 2.9 35.3 + - - +
407D GLU* 1.3 77.7 - - - +
409D LYS* 1.3 57.9 + - - +
411D LEU* 3.5 7.0 + - - +
412D LEU 3.1 10.0 + - - -
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Residues in contact with LYS 409 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403D ILE* 4.0 33.7 - - + +
405D ASN 2.9 17.9 + - - +
406D ASN* 3.5 32.5 + - - +
407D GLU 3.1 0.2 - - - -
408D ASN* 1.3 79.1 - - - +
410D MET* 1.3 65.7 + - + +
412D LEU* 3.2 10.8 + - + +
413D LYS* 3.1 46.5 + - + +
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Residues in contact with MET 410 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406D ASN* 3.0 38.0 + - - +
407D GLU* 5.4 1.3 - - - -
409D LYS* 1.3 85.5 - - + +
411D LEU* 1.3 61.3 + - - +
413D LYS* 3.7 10.7 - - + +
414D ARG* 2.9 58.2 + - + +
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Residues in contact with LEU 411 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178D TRP* 3.8 17.0 - - + +
181D SER* 4.2 21.5 - - - -
182D VAL* 4.7 7.2 - - + -
407D GLU 2.8 19.4 + - - +
408D ASN* 3.5 8.1 - - - +
410D MET* 1.3 77.2 - - - +
412D LEU* 1.3 58.0 + - - +
414D ARG* 3.2 21.9 + - + +
415D MET* 2.8 55.2 + - + +
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Residues in contact with LEU 412 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D ASN* 5.2 2.9 - - + +
175D PHE* 4.5 10.8 - - + +
178D TRP* 3.4 50.4 - - + +
399D TYR* 4.4 4.0 - - + -
403D ILE* 4.3 21.5 - - + -
408D ASN 3.1 4.3 + - - +
409D LYS* 3.2 9.6 + - + +
411D LEU* 1.3 78.9 - - - +
413D LYS* 1.3 65.9 + - + +
415D MET* 3.3 6.6 + - + +
416D GLN* 2.9 35.1 + - - +
455D THR* 3.7 37.0 - - + +
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Residues in contact with LYS 413 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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409D LYS* 3.1 39.0 + - + +
410D MET* 3.5 8.9 + - + +
411D LEU 3.3 0.4 - - - -
412D LEU* 1.3 83.0 - - + +
414D ARG* 1.3 61.6 + - - +
416D GLN* 3.1 21.8 + - - +
455D THR* 5.1 13.5 + - - +
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Residues in contact with ARG 414 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407D GLU* 3.9 11.7 + - - +
410D MET* 2.9 58.6 + - + +
411D LEU* 3.5 33.4 - - + +
413D LYS* 1.3 76.6 - - - +
415D MET* 1.3 61.5 + - + +
416D GLN* 3.1 4.4 + - - +
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Residues in contact with MET 415 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D ASN* 2.7 41.4 + - - +
177D ASN* 3.8 13.0 - - + +
178D TRP* 3.7 40.2 - - + +
181D SER* 4.7 5.6 - - - +
214D LYS* 6.2 0.2 - - - -
411D LEU* 2.8 46.9 + - + +
412D LEU* 3.6 7.0 - - + +
414D ARG* 1.3 75.0 - - + +
416D GLN* 1.3 75.8 + - - +
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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