Contacts of the helix formed by residues 614 - 620 (chain D) in PDB entry 5T46
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 614 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128C ARG* 6.3 0.2 - - - +
132C GLU* 2.8 39.0 + - - +
135C LEU* 4.2 13.1 - - + +
186C ARG* 3.6 32.7 - - - +
303C GOL 3.5 19.3 + - - -
613D ASP* 1.3 75.5 - - + +
615D GLU* 1.3 83.3 + - - +
617D LEU* 3.2 4.1 + - - +
618D LEU* 2.8 60.3 + - - +
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Residues in contact with GLU 615 (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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613D ASP* 3.3 23.8 - - - +
614D ARG* 1.3 99.2 + - + +
616D PHE* 1.3 63.7 + - - +
618D LEU* 3.9 6.7 - - + +
619D GLY* 3.1 20.8 + - - -
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Residues in contact with PHE 616 (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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37C HIS* 4.6 12.3 - + - -
69C VAL* 4.4 7.6 - - + -
612D TYR* 3.2 51.1 - + + -
613D ASP* 2.8 26.8 + - - +
615D GLU* 1.3 78.4 - - - +
617D LEU* 1.3 66.3 + - + +
619D GLY* 3.3 5.2 + - - -
620D PHE* 3.1 52.2 - + - -
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Residues in contact with LEU 617 (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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39C LEU* 4.8 0.4 - - + -
69C VAL* 3.9 31.0 - - + -
73C TRP* 2.9 25.2 + - + +
135C LEU* 3.7 51.8 - - + +
138C ILE* 4.0 20.4 - - + -
139C GLY* 4.1 3.4 - - - -
186C ARG* 5.8 0.2 - - - +
612D TYR* 3.8 30.5 - - + +
613D ASP 3.1 15.9 + - - +
614D ARG* 3.8 4.9 - - - +
616D PHE* 1.3 77.6 - - + +
618D LEU* 1.3 63.8 + - - +
620D PHE* 3.1 11.7 + - - +
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Residues in contact with LEU 618 (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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73C TRP* 3.8 26.0 - - + -
131C LEU* 4.6 9.0 - - + -
135C LEU* 4.2 13.7 - - + -
614D ARG* 2.8 64.2 + - - +
615D GLU* 4.1 5.2 - - + +
617D LEU* 1.3 72.8 - - - +
619D GLY* 1.3 62.3 + - - +
620D PHE 3.0 1.6 + - - -
621D GLN* 3.1 27.9 + - - +
622D PHE* 4.9 1.7 + - - -
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Residues in contact with GLY 619 (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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615D GLU 3.1 14.2 + - - -
616D PHE 3.3 5.8 + - - -
617D LEU 3.1 1.0 - - - -
618D LEU* 1.3 77.0 - - - +
620D PHE* 1.3 63.0 + - - +
621D GLN 3.4 0.4 + - - -
622D PHE 4.8 1.4 + - - -
623D ILE* 3.9 13.0 - - - +
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Residues in contact with PHE 620 (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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34C TYR* 3.7 4.5 - - - -
37C HIS* 3.5 37.5 - + - -
69C VAL* 3.7 26.0 - - + -
70C GLU* 3.7 14.1 - - + -
73C TRP* 3.8 2.9 - - + -
616D PHE* 3.1 61.2 - + - -
617D LEU 3.1 6.6 + - - +
618D LEU 3.0 1.2 - - - -
619D GLY* 1.3 80.9 - - - +
621D GLN* 1.3 61.6 + - - +
622D PHE 3.1 3.9 + - - -
623D ILE* 3.4 25.3 - - + +
626D SER* 2.7 27.8 + - - +
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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