Contacts of the helix formed by residues 78 - 87 (chain I) 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 78 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59I PRO* 4.3 9.0 - - + +
60I GLY* 3.6 28.7 - - - +
75I ARG* 5.1 1.6 - - - +
77I ARG* 1.3 73.3 - - - +
79I GLU* 1.3 66.9 + - - +
80I ALA* 3.4 10.5 - - - +
81I ASP* 3.0 31.6 + - - +
82I ILE* 2.9 27.3 + - - +
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Residues in contact with GLU 79 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78I THR* 1.3 72.0 - - - +
80I ALA* 1.3 59.2 + - - +
82I ILE* 2.9 12.1 + - + +
83I GLU* 2.7 40.8 + - - +
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Residues in contact with ALA 80 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78I THR* 3.4 11.4 - - - +
79I GLU* 1.3 80.0 - - - +
81I ASP* 1.3 66.4 + - - +
83I GLU* 3.3 16.6 - - - +
84I LEU* 3.4 19.5 + - + +
167K ASP* 6.1 1.3 - - - +
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Residues in contact with ASP 81 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75I ARG* 3.0 34.4 + - - -
77I ARG* 3.6 19.4 + - + -
78I THR* 3.0 40.2 + - - +
79I GLU 3.0 0.2 - - - -
80I ALA* 1.3 81.1 - - - +
82I ILE* 1.3 64.7 + - - +
83I GLU 3.1 0.7 + - - -
84I LEU* 3.4 1.7 + - - -
85I GLY 3.2 15.8 + - - -
140I VAL* 4.3 16.2 - - - +
145I GLY 4.8 5.4 - - - +
158I SER* 3.3 21.7 + - - -
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Residues in contact with ILE 82 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77I ARG* 3.9 27.1 - - + +
78I THR 2.9 17.5 - - - +
79I GLU* 2.9 13.8 + - + +
81I ASP* 1.3 71.6 - - - +
83I GLU* 1.3 66.4 + - - +
85I GLY 3.5 0.5 + - - -
86I ARG* 3.2 43.7 + - - +
111I ASP* 3.8 0.7 - - - +
119I ALA* 3.5 26.9 - - + +
120I GLY 3.4 19.3 - - - +
121I GLU* 4.0 11.9 - - + +
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Residues in contact with GLU 83 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79I GLU* 2.7 24.8 + - - +
80I ALA* 3.3 9.4 - - - +
82I ILE* 1.3 70.1 - - - +
84I LEU* 1.3 69.0 + - + +
86I ARG* 2.7 21.3 + - - +
87I SER* 3.1 13.6 + - - -
83R GLU* 5.3 5.0 - - - +
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Residues in contact with LEU 84 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80I ALA* 3.4 18.5 + - + +
81I ASP* 3.9 2.9 - - - +
83I GLU* 1.3 80.9 - - + +
85I GLY* 1.3 64.4 + - - +
87I SER* 2.8 29.0 + - - +
88I VAL* 3.4 13.1 + - + +
144I PHE* 4.1 22.4 - - - +
145I GLY* 4.5 11.0 - - - +
157I ASP* 6.2 0.4 - - + -
158I SER* 3.7 13.9 - - - +
89R GLN* 6.2 2.2 - - - +
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Residues in contact with GLY 85 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77I ARG* 4.5 0.7 - - - -
81I ASP 3.2 7.4 + - - -
82I ILE 3.9 0.2 - - - -
83I GLU 2.8 4.2 + - - -
84I LEU* 1.3 78.3 - - - +
86I ARG* 1.3 59.8 + - - +
88I VAL* 3.4 8.0 + - - +
111I ASP* 3.3 28.9 + - - +
157I ASP* 6.2 0.2 - - - -
158I SER* 3.6 10.5 + - - -
159I ALA* 4.9 1.3 - - - -
161I ARG* 3.0 31.6 + - - -
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Residues in contact with ARG 86 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82I ILE* 3.2 30.0 - - - +
83I GLU* 2.7 12.4 + - - +
85I GLY* 1.3 69.6 - - - -
87I SER* 1.3 56.0 + - - +
88I VAL 3.1 13.7 + - - +
89I GLN* 4.7 4.3 + - - -
111I ASP* 3.2 30.5 + - + +
112I GLN* 3.4 40.2 + - - +
115I THR* 4.9 0.6 + - - -
118I GLU 3.3 24.0 + - - -
119I ALA* 4.1 6.5 + - - +
120I GLY* 3.9 13.7 - - - +
87R SER* 5.5 0.3 - - - -
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Residues in contact with SER 87 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83I GLU* 3.1 13.4 + - - -
84I LEU* 2.8 25.2 + - - +
86I ARG* 1.3 76.2 - - - +
88I VAL* 1.3 58.5 + - - +
89I GLN* 3.8 4.6 + - - -
92I GLN* 3.1 13.0 + - - -
87R SER* 3.2 36.8 - - - +
89R GLN* 3.3 17.2 + - - -
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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