Contacts of the helix formed by residues 82 - 91 (chain C) in PDB entry 2V5Q
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 82 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52C HIS* 3.7 2.2 - - - -
73C VAL 4.4 4.3 - - - -
74C ASP* 3.7 30.2 + - + +
75C ALA 3.4 2.9 - - - +
76C ALA* 4.9 2.9 - - + -
80C GLY 4.5 4.5 - - - +
81C PHE* 1.3 76.5 - - - +
83C PRO* 1.3 77.5 - - - +
84C LEU* 3.0 12.9 + - - +
85C HIS* 3.0 35.0 + - - +
86C LEU* 3.2 12.8 + - - +
105C ASP 5.3 0.2 + - - -
108C ALA* 3.8 26.2 - - + +
109C PHE 5.9 0.4 - - - +
116C PRO* 4.8 0.3 - - - +
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Residues in contact with PRO 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C THR* 4.7 0.7 - - - +
51C LEU* 3.8 40.6 - - + +
52C HIS* 3.6 28.9 - - + +
55C ALA* 3.6 5.1 - - + +
72C ASP 4.7 1.8 - - - +
73C VAL 3.3 23.3 - - - +
75C ALA 3.4 13.7 - - - +
82C THR* 1.3 82.9 - - - +
84C LEU* 1.3 49.2 + - - +
86C LEU* 3.2 4.9 + - + +
87C ALA* 2.8 33.4 + - - +
99C LEU* 3.7 16.4 - - + -
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Residues in contact with LEU 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C VAL 5.1 0.2 + - - -
74C ASP* 5.9 0.2 - - - +
82C THR* 3.0 11.8 + - - +
83C PRO* 1.3 76.0 - - - +
85C HIS* 1.3 56.3 - - - +
87C ALA 4.4 0.2 - - - +
88C ALA* 2.8 32.8 + - + +
96C VAL* 3.9 34.5 - - + +
99C LEU* 3.7 13.1 - - + +
100C LEU* 4.0 14.4 - - + -
104C ALA* 4.1 17.5 - - + -
105C ASP 3.6 25.6 - - - +
106C VAL* 3.8 15.3 - - - -
116C PRO* 3.8 14.6 - - + -
132C LEU* 4.1 15.3 - - + -
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Residues in contact with HIS 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C GLY 3.8 8.3 - - - -
81C PHE* 3.7 20.6 - + + -
82C THR* 3.0 34.8 + - + +
84C LEU* 1.3 77.1 - - - +
86C LEU* 1.3 58.8 + - - +
88C ALA* 3.8 1.6 - - - +
89C MET* 2.9 31.7 + - - +
108C ALA* 3.3 33.7 + - + -
109C PHE 3.9 0.2 - - - -
110C ASP* 3.7 17.4 + - + +
114C SER 2.8 23.2 + - - -
115C THR 3.6 5.6 - - - -
116C PRO* 3.5 23.2 - - + +
119C LEU* 3.7 20.8 - - + +
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Residues in contact with LEU 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320B THR* 4.2 10.5 - - + +
48C LEU* 3.9 13.5 - - + -
52C HIS* 3.7 43.3 - - + +
56C VAL* 3.9 24.1 - - + +
77C ASP* 4.8 0.9 - - - +
81C PHE* 3.7 32.3 - - + -
82C THR 3.2 9.2 + - - +
83C PRO* 3.2 8.6 + - + +
84C LEU 3.2 0.4 - - - -
85C HIS* 1.3 78.4 - - - +
87C ALA* 1.3 56.7 + - - +
89C MET* 3.6 24.1 + - + +
90C THR* 2.7 39.0 + - - +
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Residues in contact with ALA 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C ALA* 4.3 8.6 - - + +
83C PRO 2.8 15.8 + - - +
84C LEU 3.9 2.5 - - - +
86C LEU* 1.3 76.0 - - - +
88C ALA* 1.3 64.2 + - - +
90C THR* 3.3 6.5 + - - -
91C GLY 3.0 18.7 + - - -
92C HIS* 3.2 13.1 + - + +
95C ILE* 3.6 32.5 - - + -
96C VAL* 3.9 17.4 - - + +
99C LEU* 4.0 5.2 - - + -
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Residues in contact with ALA 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C LEU* 2.8 21.9 + - + +
85C HIS 3.8 2.0 - - - +
87C ALA* 1.3 73.4 - - - +
89C MET* 1.3 63.2 + - - +
90C THR 3.2 1.0 + - - -
91C GLY* 3.2 10.2 + - - -
96C VAL* 3.9 4.6 - - + +
116C PRO* 3.4 34.8 - - + +
120C ALA* 3.8 11.8 - - + +
125C HIS* 3.5 10.6 - - - +
128C ILE* 3.8 24.7 - - + +
132C LEU* 4.0 2.5 - - + -
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Residues in contact with MET 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316B ILE* 3.8 32.5 - - + +
317B THR* 3.5 36.5 - - + +
320B THR* 4.3 9.6 - - - +
321B ILE* 4.9 1.1 - - + -
56C VAL* 4.0 20.2 - - + -
81C PHE* 5.2 3.4 - - - -
85C HIS 2.9 17.4 + - - +
86C LEU* 3.7 29.4 - - + +
88C ALA* 1.3 75.6 - - - +
90C THR* 1.3 65.4 + - + +
119C LEU* 4.1 26.3 - - + +
123C GLU* 3.3 10.8 - - + +
125C HIS* 3.2 16.7 + - - -
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Residues in contact with THR 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317B THR* 4.9 1.6 - - + -
321B ILE* 3.7 25.8 - - + -
55C ALA 4.2 0.2 + - - -
56C VAL* 3.7 24.1 + - + +
86C LEU 2.7 22.2 + - - +
87C ALA* 3.3 3.3 + - - -
88C ALA 3.2 0.2 - - - -
89C MET* 1.3 84.4 - - + +
91C GLY* 1.3 62.3 + - - +
92C HIS* 2.9 40.5 + - - -
125C HIS* 3.5 12.4 + - - -
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Residues in contact with GLY 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C ALA 3.0 4.0 + - - -
88C ALA 3.2 3.6 + - - -
90C THR* 1.3 79.9 - - - +
92C HIS* 1.3 60.2 + - - +
93C LEU* 3.3 7.6 + - - +
125C HIS* 3.4 27.3 - - - -
128C ILE* 3.8 17.3 - - - +
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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