Contacts of the helix formed by residues 475 - 484 (chain B) in PDB entry 5DO7
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 ARG 475 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B HIS* 3.3 32.5 + - - +
155B ASN 3.2 22.8 + - - +
156B GLN* 3.2 21.6 + - + +
472B TYR 4.4 1.0 + - - +
473B SER 3.9 4.9 + - - +
474B GLU* 1.3 71.4 - - - +
476B ALA* 1.3 71.8 + - - +
477B MET* 3.0 3.8 - - - -
478B LEU* 2.8 23.2 + - - +
479B TYR* 3.6 28.1 + - - -
667B GLN* 5.5 4.0 - - - -
668B LYS 5.5 0.4 - - - -
669B PRO* 3.8 42.1 - - + +
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Residues in contact with ALA 476 (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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156B GLN* 4.2 30.0 - - + +
158B LEU* 5.5 7.0 - - + -
474B GLU* 3.5 11.4 - - + -
475B ARG* 1.3 83.5 - - - +
477B MET* 1.3 65.1 + - - +
479B TYR* 2.8 20.0 + - - +
480B TYR* 2.8 33.3 + - + +
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Residues in contact with MET 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B CYS* 3.7 33.0 - - - +
474B GLU* 4.0 26.7 - - + +
475B ARG 2.8 4.6 + - - +
476B ALA* 1.3 76.7 - - - +
478B LEU* 1.3 50.9 + - - +
480B TYR* 2.9 14.5 + - + +
481B GLU* 2.5 38.0 + - - +
486B LEU* 6.0 0.7 - - + -
492B TYR* 3.0 51.6 - - + +
496B LYS* 4.1 6.1 - - - +
658B TYR* 4.8 2.0 - - - +
662B LEU* 4.8 12.6 - - + -
667B GLN* 4.5 20.6 - - + +
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Residues in contact with LEU 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ARG* 5.9 0.9 - - - +
475B ARG* 2.8 17.9 + - - +
477B MET* 1.3 72.7 - - - +
479B TYR* 1.3 79.3 + - + +
481B GLU* 2.8 37.1 + - - +
482B LEU* 2.8 28.8 + - + +
666B LYS* 4.7 5.2 - - + -
667B GLN* 3.5 24.9 + - - +
668B LYS* 3.5 46.0 - - + +
669B PRO* 3.7 19.7 - - + -
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Residues in contact with TYR 479 (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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121B ARG* 3.5 30.0 + - - -
152B ARG* 3.0 47.5 + - + -
154B HIS* 3.3 16.7 - + - -
156B GLN* 3.7 29.6 - - + +
475B ARG* 3.6 30.1 - - - -
476B ALA 2.8 11.3 + - - +
478B LEU* 1.3 90.9 - - + +
480B TYR* 1.3 60.7 + - + +
482B LEU* 4.6 4.0 - - + +
483B GLU* 2.8 46.9 + - + +
669B PRO* 5.0 5.2 - - + +
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Residues in contact with TYR 480 (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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156B GLN* 4.5 14.1 + - + -
158B LEU* 4.9 8.2 - - + +
166B THR* 6.2 0.3 - - - +
170B ILE* 4.7 18.2 - - + -
173B MET* 5.7 0.2 - - + -
225B VAL* 6.1 3.8 - - + -
405B ARG* 2.7 45.7 + - - -
476B ALA* 2.8 29.2 + - + +
477B MET* 2.9 25.0 + - + +
479B TYR* 1.3 75.5 - - + +
481B GLU* 1.3 64.6 + - - +
483B GLU* 4.8 3.4 - - + -
484B ASP* 2.8 20.8 + - - -
485B GLY* 3.2 12.0 + - - +
486B LEU* 2.8 37.7 + - + -
492B TYR* 5.5 3.1 - + - -
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Residues in contact with GLU 481 (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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145B ARG* 5.4 2.1 - - - -
477B MET 2.5 21.1 + - - +
478B LEU* 2.8 30.0 + - - +
480B TYR* 1.3 73.7 - - - +
482B LEU* 1.3 80.3 + - - +
484B ASP* 3.3 10.9 + - - -
486B LEU* 4.7 12.2 - - - +
666B LYS* 4.8 12.5 - - - +
667B GLN 5.6 0.2 + - - -
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Residues in contact with LEU 482 (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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121B ARG* 3.8 51.4 - - + +
145B ARG* 3.6 25.0 - - - +
478B LEU* 2.8 42.7 + - + +
479B TYR* 4.3 4.0 - - + +
481B GLU* 1.3 96.0 - - - +
483B GLU* 1.3 63.9 + - + +
484B ASP 3.4 0.5 + - - -
668B LYS* 4.7 7.0 - - - +
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Residues in contact with GLU 483 (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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121B ARG* 4.8 12.1 + - - -
145B ARG* 4.1 9.8 - - - +
148B VAL 5.0 5.7 - - - +
150B HIS* 3.3 40.0 + - - +
152B ARG* 5.8 0.5 - - - +
174B ARG* 2.5 36.7 + - - +
226B GLN* 3.9 21.4 + - - +
229B TRP* 5.9 0.5 - - - -
479B TYR* 2.8 43.0 + - + +
480B TYR* 4.3 3.8 - - + +
482B LEU* 1.3 74.8 - - + +
484B ASP* 1.3 65.1 + - - +
485B GLY 3.7 1.8 - - - +
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Residues in contact with ASP 484 (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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145B ARG* 3.2 44.7 + - - +
146B LYS* 3.9 13.5 + - - -
173B MET 5.7 0.5 - - - +
174B ARG* 4.7 12.2 + - - +
398B GLN* 5.0 3.3 + - - -
480B TYR 2.8 11.2 + - - -
481B GLU 3.6 7.4 - - - +
482B LEU 3.3 1.2 - - - -
483B GLU* 1.3 81.9 - - - +
485B GLY* 1.3 63.0 + - - +
486B LEU* 3.3 7.7 + - - +
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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