Contacts of the helix formed by residues 110 - 114 (chain L) in PDB entry 2QJK
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 THR 110 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172E ALA* 4.1 28.5 - - + -
88L VAL 6.1 0.9 - - - -
90L LEU* 4.5 2.7 - - + -
108L GLU* 2.4 31.5 + - + +
109L ALA* 1.3 74.2 - - - +
111L ASP* 1.3 66.5 + - - +
112L GLN* 3.2 22.5 + - - +
113L ASN* 2.7 42.2 + - - +
114L ARG* 3.5 4.2 + - - +
161L ARG* 4.1 0.7 - - - +
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Residues in contact with ASP 111 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77L ARG* 2.6 45.5 + - - -
82L ILE 4.1 0.9 - - - +
85L GLY* 3.5 32.0 + - - +
86L ARG* 3.2 37.3 + - + +
110L THR* 1.3 71.6 - - - +
112L GLN* 1.3 63.8 + - - +
114L ARG* 3.2 17.9 + - - +
115L THR* 3.6 10.1 + - - +
159L ALA* 4.1 5.1 - - + +
161L ARG* 3.3 14.0 - - - +
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Residues in contact with GLN 112 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86L ARG* 3.7 40.6 + - - +
110L THR* 2.7 31.6 + - - +
111L ASP* 1.3 82.4 - - - +
113L ASN* 1.3 61.3 + - - +
114L ARG 3.2 1.3 + - - -
115L THR* 3.6 19.0 + - - +
117L ASP 4.9 2.1 - - - +
118L GLU* 5.2 5.6 - - - +
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Residues in contact with ASN 113 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98L ALA* 4.0 7.3 - - + +
100L ASN* 2.9 27.3 + - - +
103L ILE* 3.6 28.1 - - + +
107L ALA* 3.9 4.0 - - - +
108L GLU* 2.8 43.3 + - - +
110L THR* 2.7 22.2 + - - +
112L GLN* 1.3 74.8 - - - +
114L ARG* 1.3 58.9 + - + -
115L THR 3.6 1.1 - - - -
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Residues in contact with ARG 114 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98L ALA* 2.7 42.9 + - - +
99L ARG* 4.1 1.0 - - - +
100L ASN* 4.6 0.6 + - - -
109L ALA* 4.6 3.6 - - - +
110L THR 3.7 14.1 - - - +
111L ASP* 3.2 9.7 + - - +
113L ASN* 1.3 81.4 - - - +
115L THR* 1.3 64.7 + - + +
123L LEU* 3.4 19.5 - - + +
124L VAL 4.7 2.8 + - - +
125L MET* 3.9 7.9 - - - -
159L ALA* 2.8 46.0 + - + +
160L GLY* 2.8 27.4 + - - -
161L ARG* 3.9 13.8 - - - +
170L ASN* 3.7 14.0 - - - +
171L LEU 2.9 27.1 + - - -
173L ILE* 3.4 28.7 - - - +
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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