Contacts of the helix formed by residues 110 - 115 (chain B) in PDB entry 3NDM
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 PHE 110 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B SER* 2.9 9.2 + - - +
109B LYS* 1.3 77.8 - - - +
111B GLU* 1.3 74.7 + - - +
113B ILE* 2.7 14.9 + - - +
114B LYS* 3.0 32.7 + - + -
147B ARG* 4.1 3.2 + - - +
379B GLU* 3.2 39.9 - - + +
380B THR 2.9 36.1 - - - -
381B PHE* 3.2 43.8 - + + -
382B PRO* 4.3 7.9 - - + -
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Residues in contact with GLU 111 (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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86B ALA 4.7 13.9 - - - +
87B PHE* 4.3 15.0 - - + +
108B SER* 3.1 25.8 + - - +
110B PHE* 1.3 81.3 - - + +
112B MET* 1.3 55.3 + - - +
113B ILE 2.8 2.4 + - - -
114B LYS* 2.9 9.2 + - - +
115B ARG* 2.7 71.2 + - + +
378B GLU* 4.5 19.9 - - + +
379B GLU* 3.9 30.5 + - + +
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Residues in contact with MET 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B PHE* 3.7 22.9 - - + -
107B LEU* 3.4 27.6 - - + -
108B SER 2.8 25.4 + - - +
109B LYS* 4.0 7.9 - - - +
111B GLU* 1.3 76.2 - - - +
113B ILE* 1.3 58.6 + - - +
115B ARG* 3.3 12.0 - - - +
116B SER 5.0 0.2 - - - +
117B ASP 3.6 3.3 - - - +
118B SER* 3.0 26.6 - - - -
120B PHE* 3.3 40.6 - - + -
121B PHE* 3.5 27.6 - - + -
149B LEU* 4.4 7.4 - - + -
394B PHE* 4.3 6.7 - - + -
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Residues in contact with ILE 113 (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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51A ASN* 4.2 19.3 - - - +
109B LYS 3.2 15.0 + - - +
110B PHE 2.7 9.4 + - - +
112B MET* 1.3 81.9 - - - +
114B LYS* 1.3 61.3 + - - +
115B ARG 2.7 18.0 - - - +
116B SER* 4.9 0.7 - - - +
118B SER* 4.3 13.0 - - - +
381B PHE* 3.8 21.1 - - + -
390B ASN* 4.0 24.2 - - - +
393B PRO* 4.5 8.3 - - + -
394B PHE* 4.4 13.9 - - + -
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Residues in contact with LYS 114 (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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110B PHE* 3.0 36.1 + - + +
111B GLU* 2.9 15.3 + - - +
113B ILE* 1.3 79.4 - - - +
115B ARG* 1.3 101.2 + - - +
116B SER* 3.8 1.2 + - - -
379B GLU* 4.4 15.0 + - + -
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Residues in contact with ARG 115 (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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87B PHE* 3.6 33.7 - - + -
111B GLU* 2.7 44.2 + - - +
112B MET* 3.3 8.6 - - - +
113B ILE 2.7 19.6 - - - +
114B LYS* 1.3 115.4 + - + +
116B SER* 1.3 67.3 + - - +
117B ASP 3.3 2.3 + - - +
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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