Contacts of the helix formed by residues 405 - 410 (chain D) in PDB entry 5EIB
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 LEU 405 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185D TYR* 3.8 18.6 - - + +
399D PHE* 3.7 32.5 - - + -
402D LYS* 3.5 35.2 + - + +
403D ALA 3.0 2.8 + - - -
404D PHE* 1.3 76.7 - - - +
406D HIS* 1.3 58.4 + - - +
408D TYR* 2.9 23.9 + - - +
409D THR* 3.1 17.6 + - + +
415D GLU* 3.3 37.7 - - + +
418D PHE* 3.8 25.1 - - + -
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Residues in contact with HIS 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 PHE* 4.3 6.5 - - - -
405D LEU* 1.3 78.6 - - - +
407D TRP* 1.3 90.5 + + - +
409D THR* 3.3 12.6 - - - +
410D GLY* 2.8 29.8 + - - -
23E ARG* 4.6 15.3 - - - -
57E TYR* 2.9 33.8 + + - -
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Residues in contact with TRP 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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100D GLY 5.6 6.7 - - - -
101D ASN* 6.1 1.6 - - + -
102D ASN* 2.8 33.5 + - + +
182D VAL* 4.4 23.3 - - + -
404D PHE* 3.1 46.5 + + + +
406D HIS* 1.3 121.9 + + - +
408D TYR* 1.3 65.6 + + + +
410D GLY* 4.3 1.6 + - - -
411D GLU* 3.9 10.4 - - - +
57E TYR* 4.4 9.6 - + - -
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Residues in contact with TYR 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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101D ASN 3.8 4.5 + - - -
102D ASN* 3.8 12.3 - - - -
103D TRP* 3.9 17.0 - - + -
104D ALA* 3.8 13.9 - - + +
182D VAL* 3.4 27.6 - - + +
185D TYR* 3.6 24.3 - + + +
186D ASN* 2.6 30.9 + - - -
189D LEU* 4.2 7.9 - - + -
404D PHE 3.5 16.8 - - - -
405D LEU* 2.9 9.0 + - - +
407D TRP* 1.3 85.6 - + + +
409D THR* 1.3 65.4 + - - +
410D GLY 3.1 1.3 - - - -
411D GLU* 3.0 17.0 + - - +
413D MET* 3.5 24.8 - - + +
418D PHE* 3.5 31.9 - + + -
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Residues in contact with THR 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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405D LEU* 3.1 12.1 + - + +
406D HIS* 3.3 22.2 - - - +
408D TYR* 1.3 78.0 - - + +
410D GLY* 1.3 53.8 + - - +
412D GLY* 2.8 25.1 + - - -
413D MET* 3.4 23.5 - - + +
414D ASP 4.8 0.2 - - - -
415D GLU* 4.3 27.6 - - + +
418D PHE* 5.7 1.6 - - + -
372F LYS* 5.8 1.7 - - - +
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Residues in contact with GLY 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 HIS 2.8 18.7 + - - -
407D TRP 4.7 1.6 - - - -
408D TYR 3.1 0.4 - - - -
409D THR* 1.3 78.3 + - - +
411D GLU* 1.3 65.8 + - - +
412D GLY 3.2 0.9 + - - -
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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