Contacts of the helix formed by residues 115 - 119 (chain B) in PDB entry 6DWM
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 ILE 115 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111B THR 3.7 15.9 - - - +
112B PHE* 3.3 12.8 + - + +
114B LEU* 1.3 74.5 - - - +
116B SER* 1.3 76.1 + - - +
117B ASN 3.2 1.8 - - - -
118B GLY* 3.0 13.2 + - - -
120B SER* 3.8 11.2 - - - +
123B PHE* 3.9 32.5 - - + -
224B PHE* 3.8 21.5 - - + -
228B VAL* 3.9 17.7 - - + -
251B PHE* 3.8 15.3 - - + -
255B ASN* 3.5 9.0 - - - +
602B HJJ 3.5 30.7 - - + -
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Residues in contact with SER 116 (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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114B LEU 3.9 1.8 + - - -
115B ILE* 1.3 74.0 - - - +
117B ASN* 1.3 69.9 + - - +
119B GLN* 2.9 15.6 + - - +
120B SER* 3.8 18.2 - - - -
255B ASN* 4.2 7.1 + - - +
259B TYR* 3.5 28.7 + - - -
309B ASN* 3.9 7.7 + - - -
312B LEU* 3.8 8.2 - - - +
313B ASP* 3.3 20.1 + - - -
602B HJJ 3.3 16.2 - - - -
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Residues in contact with ASN 117 (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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113B THR 4.2 2.7 - - - -
114B LEU 4.5 4.5 + - - -
115B ILE 3.2 1.2 - - - -
116B SER* 1.3 78.0 - - - +
118B GLY* 1.3 61.2 + - - +
119B GLN* 3.1 18.3 + - - +
259B TYR* 3.6 26.4 - - + +
305B GLU* 3.1 21.5 + - - +
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Residues in contact with GLY 118 (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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112B PHE 4.5 1.8 - - - -
113B THR* 3.3 33.0 + - - -
115B ILE 3.0 9.8 + - - -
117B ASN* 1.3 77.1 - - - +
119B GLN* 1.3 60.0 + - - +
120B SER 3.6 3.3 + - - -
124B SER* 4.2 12.4 - - - -
125B PRO* 5.5 1.6 - - - +
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Residues in contact with GLN 119 (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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116B SER 2.9 11.3 + - - +
117B ASN* 3.5 17.6 + - - +
118B GLY* 1.3 82.2 - - - +
120B SER* 1.3 60.7 + - - +
124B SER* 4.7 3.6 - - - -
134B ARG* 2.8 27.1 + - - +
303B SER* 4.1 3.8 + - - -
305B GLU* 2.8 38.2 + - - +
306B LYS* 3.4 39.7 - - + +
309B ASN* 2.9 13.6 + - - +
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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