Contacts of the helix formed by residues 112 - 116 (chain G) in PDB entry 3REK
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 GLN 112 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A ASN* 4.9 7.6 - - + +
109A LEU* 4.0 26.0 - - + +
112A ILE* 3.7 31.4 - - + +
42B GLY 5.6 0.4 + - - -
129E ARG* 4.7 13.3 + - - +
110G ASN* 4.2 22.0 + - - +
111G ILE* 1.3 88.7 - - - +
113G SER* 1.3 67.7 + - - +
114G VAL* 3.5 3.8 - - + -
115G LEU* 3.4 18.2 + - + +
116G LEU* 4.0 2.1 + - - +
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Residues in contact with SER 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111G ILE 3.6 1.9 + - - -
112G GLN* 1.3 73.1 + - - +
114G VAL* 1.3 55.2 + - - +
115G LEU 2.8 11.8 + - - -
116G LEU* 2.8 35.4 + - - +
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Residues in contact with VAL 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A ILE* 3.8 43.5 - - + -
116A ARG 5.4 0.4 - - - +
117A VAL* 4.5 14.3 - - + +
44B LYS* 5.0 0.9 + - - -
112G GLN* 4.6 3.1 - - + -
113G SER* 1.3 75.8 - - - +
115G LEU* 1.3 71.4 + - + +
116G LEU 3.3 6.0 + - - +
118G LYS* 5.9 2.6 - - - +
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Residues in contact with LEU 115 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LEU* 3.4 12.8 - - + +
51A ILE* 4.9 0.9 - - + -
108A ASN* 3.7 14.8 - - - +
112A ILE* 4.6 7.0 - - + -
117A VAL* 3.9 40.4 - - + +
42B GLY 3.3 26.5 - - - +
44B LYS* 2.6 48.9 + - + +
111G ILE* 4.3 12.1 - - + -
112G GLN* 3.8 22.7 - - + +
113G SER 2.8 1.2 + - - -
114G VAL* 1.3 90.2 - - + +
116G LEU* 1.3 62.2 + - - +
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Residues in contact with LEU 116 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LEU* 4.6 2.0 - - + -
52A ARG* 4.1 22.4 - - - +
44B LYS* 4.8 1.1 + - - -
111G ILE* 4.2 23.1 - - + +
112G GLN 4.2 5.2 - - - +
113G SER* 2.8 26.3 + - - +
114G VAL 4.0 6.8 - - - +
115G LEU* 1.3 80.1 - - - +
117G PRO* 1.3 80.8 - - + +
118G LYS* 3.6 8.0 + - - +
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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