Contacts of the helix formed by residues 732 - 740 (chain B) in PDB entry 5NC5
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 ASP 732 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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730B ASP 3.6 1.4 + - - +
731B ILE* 1.4 69.6 - - - +
733B GLN* 1.3 68.6 + - - +
734B GLU* 3.3 9.6 + - - +
735B LYS* 3.1 31.9 + - + +
736B ALA* 3.1 20.6 + - - +
804B PHE* 2.9 20.2 + - - +
145D PHE* 3.7 45.8 - - + +
147D LYS* 5.9 3.3 - - - +
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Residues in contact with GLN 733 (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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210A GLN* 3.4 36.8 + - - +
237A GLN* 3.7 28.3 - - - +
250A LEU* 3.9 14.4 - - + -
731B ILE* 3.4 19.0 + - - +
732B ASP* 1.3 74.7 + - - +
734B GLU* 1.3 57.3 + - - +
736B ALA* 3.1 7.0 + - - +
737B GLN* 2.9 39.6 + - - +
743B ILE* 3.2 37.7 - - - +
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Residues in contact with GLU 734 (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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250A LEU* 3.4 20.3 - - + +
253A VAL* 4.4 16.3 - - + +
257A GLY 4.2 10.7 - - - +
259A ARG* 3.5 35.4 + - - +
732B ASP* 3.3 9.3 + - - +
733B GLN* 1.3 79.6 - - - +
735B LYS* 1.3 64.5 + - - +
737B GLN* 3.4 2.6 + - - +
738B ALA* 3.0 25.2 + - + +
147D LYS* 3.3 32.5 + - - -
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Residues in contact with LYS 735 (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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732B ASP* 3.1 29.4 + - + +
733B GLN 3.3 0.2 - - - -
734B GLU* 1.3 77.4 - - - +
736B ALA* 1.3 62.7 + - - +
738B ALA* 3.2 8.0 + - + -
739B LEU* 3.0 57.7 + - + +
803B ALA* 3.6 27.1 - - - +
804B PHE* 4.3 3.8 - - + -
144D LYS 5.7 2.4 + - - -
145D PHE* 4.7 15.7 - - + +
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Residues in contact with ALA 736 (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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731B ILE* 5.1 1.3 - - + -
732B ASP 3.1 12.8 + - - +
733B GLN* 3.1 10.0 + - - +
735B LYS* 1.3 75.9 - - - +
737B GLN* 1.3 61.1 + - - +
739B LEU* 3.3 4.4 + - - -
740B GLY 3.0 4.2 + - - -
741B VAL* 3.0 48.6 + - - +
743B ILE* 3.8 19.1 - - + -
746B ILE* 4.1 13.9 - - + -
804B PHE* 4.5 6.4 - - + +
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Residues in contact with GLN 737 (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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210A GLN* 4.2 6.5 - - - +
250A LEU* 3.3 45.1 + - - +
251A LEU 3.9 3.7 + - - +
252A LYS* 3.4 26.0 - - - -
253A VAL* 3.9 12.7 + - + -
733B GLN* 2.9 21.1 + - - +
734B GLU 3.8 4.3 - - - +
736B ALA* 1.3 77.4 - - + +
738B ALA* 1.3 63.9 + - - +
740B GLY* 3.2 12.5 + - - +
741B VAL 5.1 0.7 - - - -
743B ILE* 5.6 4.7 - - + +
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Residues in contact with ALA 738 (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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253A VAL* 5.3 8.0 - - + +
734B GLU* 3.0 21.7 + - + +
735B LYS* 3.7 13.0 - - + +
736B ALA 3.2 0.2 - - - -
737B GLN* 1.3 77.8 - - - +
739B LEU* 1.3 60.7 + - + +
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Residues in contact with LEU 739 (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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735B LYS* 3.0 54.7 + - + +
736B ALA* 3.9 0.9 - - - +
737B GLN 3.2 0.2 - - - -
738B ALA* 1.3 79.8 - - + +
740B GLY* 1.3 61.0 + - - +
741B VAL* 3.7 14.1 - - + -
793B ALA* 3.3 16.6 - - - +
795B ASP* 3.6 13.9 - - - +
799B VAL* 4.0 30.7 - - + -
803B ALA* 4.8 3.8 - - + -
804B PHE* 4.5 11.4 - - + -
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Residues in contact with GLY 740 (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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736B ALA 3.0 4.3 + - - -
737B GLN* 3.2 11.7 + - - -
738B ALA 3.3 0.4 - - - -
739B LEU* 1.3 78.4 - - - +
741B VAL* 1.3 59.3 + - - +
742B SER 4.2 0.7 + - - -
792B ARG 4.7 0.2 - - - +
793B ALA* 3.2 1.6 - - - -
794B ALA* 2.6 43.0 + - - +
795B ASP* 5.4 0.7 - - - -
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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