Contacts of the helix formed by residues 96 - 106 (chain C) in PDB entry 2BHT
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 SER 96 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94C ASN 4.1 0.6 + - - -
95C MET* 1.3 78.3 - - - +
97C GLN* 1.3 63.0 + - - +
98C GLU* 3.2 21.7 - - - +
99C ARG* 3.1 61.1 + - - +
100C ARG* 3.3 8.3 + - - +
285C ARG 4.1 1.3 - - - -
288C SER* 4.3 4.7 - - - -
289C THR* 4.7 12.1 - - - -
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Residues in contact with GLN 97 (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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97A GLN* 2.9 36.0 + - - +
95C MET 3.6 0.8 + - - -
96C SER* 1.3 71.7 - - - +
98C GLU* 1.3 77.6 + - - +
100C ARG* 3.1 23.4 - - - +
101C ALA* 2.9 26.3 + - - +
288C SER* 3.5 28.1 - - - +
99D ARG* 5.5 0.6 - - - +
287D LEU 4.7 1.3 - - - +
288D SER* 4.0 22.3 + - - +
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Residues in contact with GLU 98 (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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96C SER* 3.2 11.2 + - - +
97C GLN* 1.3 86.3 - - - +
99C ARG* 1.3 55.8 + - - +
101C ALA* 4.0 8.3 - - - -
102C ALA* 2.5 38.1 + - - +
284C ASP 3.6 6.6 - - - +
285C ARG* 2.8 50.1 - - + +
287C LEU* 3.7 0.7 + - - -
288C SER* 2.4 45.6 + - - -
99D ARG* 4.5 7.7 + - - -
284D ASP 5.1 3.1 - - - +
287D LEU* 3.4 25.4 - - + +
288D SER 5.4 0.4 - - - +
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Residues in contact with ARG 99 (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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69C SER 3.9 8.9 + - - -
70C GLY* 3.4 35.8 - - - +
71C ASN* 4.1 12.9 + - - +
74C ILE* 4.6 7.0 - - + +
91C MET* 4.2 8.7 - - - -
95C MET* 4.9 0.4 - - - -
96C SER* 3.1 39.7 + - - +
98C GLU* 1.3 74.7 - - - +
100C ARG* 1.3 66.8 + - - +
102C ALA* 3.2 8.1 + - - +
103C MET* 3.0 29.2 + - - +
207C PRO* 4.9 9.0 - - - +
281C ASP* 4.0 7.9 + - - -
285C ARG* 3.3 36.0 + - + +
286C TYR* 3.0 49.6 + - - +
289C THR* 5.5 1.0 - - - +
320C PLP 5.3 0.4 - - - +
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Residues in contact with ARG 100 (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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287B LEU 5.0 0.6 + - - -
288B SER* 2.6 26.5 + - - +
289B THR 3.5 9.4 + - - -
290B GLY* 3.5 25.1 - - - -
91C MET* 3.5 13.1 - - + +
93C ASP 3.2 21.6 + - - -
95C MET 3.9 12.3 + - - -
96C SER 3.3 12.5 + - - +
97C GLN* 3.1 18.2 + - - +
99C ARG* 1.3 80.2 - - - +
101C ALA* 1.3 55.7 + - - +
103C MET* 3.2 16.1 + - - +
104C ARG* 2.8 41.0 + - - +
110C LEU* 4.0 10.1 - - + -
112C LEU* 3.5 22.4 - - - +
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Residues in contact with ALA 101 (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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97C GLN 2.9 15.7 + - - +
98C GLU* 3.7 5.6 - - - +
100C ARG* 1.3 76.0 - - - +
102C ALA* 1.3 56.5 - - - +
104C ARG* 4.0 9.2 - - - +
105C ALA* 3.0 30.1 + - - +
287D LEU* 3.3 30.8 - - + +
292D PHE* 5.0 3.0 - - + +
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Residues in contact with ALA 102 (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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74C ILE* 3.4 29.6 - - + -
98C GLU 2.5 22.7 + - - +
99C ARG 3.3 6.3 - - - +
100C ARG 3.2 0.2 - - - -
101C ALA* 1.3 72.1 - - - +
103C MET* 1.3 67.3 + - - +
105C ALA* 3.3 17.4 + - - +
106C TYR* 3.3 18.1 - - + -
285C ARG* 4.8 3.6 - - - -
251D PHE* 4.6 7.6 - - + -
287D LEU* 3.9 15.0 - - + +
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Residues in contact with MET 103 (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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68C THR* 4.4 8.5 - - - -
70C GLY 4.4 6.3 - - - +
73C GLY* 3.7 7.9 - - - -
74C ILE* 3.4 21.8 - - + +
77C ALA* 3.9 5.1 - - - +
89C LEU* 3.3 43.1 - - + -
91C MET* 3.4 33.7 - - + +
99C ARG* 3.0 27.5 + - + +
100C ARG* 3.2 8.0 + - - +
102C ALA* 1.3 79.3 - - - +
104C ARG* 1.3 63.8 - - + +
106C TYR* 3.0 16.2 + - - +
108C ALA* 3.3 20.8 + - + +
110C LEU* 4.1 15.0 - - + -
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Residues in contact with ARG 104 (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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100C ARG* 2.8 42.0 + - - +
101C ALA* 4.3 6.3 - - - +
103C MET* 1.3 71.7 - - - +
105C ALA* 1.3 57.7 + - - +
107C GLY* 2.7 23.1 + - - -
108C ALA 3.6 16.8 - - - +
110C LEU* 3.6 34.6 - - + +
246D VAL* 5.3 0.5 - - - +
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Residues in contact with ALA 105 (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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101C ALA 3.0 20.5 + - - +
102C ALA 3.3 8.1 - - - +
103C MET 3.2 0.2 - - - -
104C ARG* 1.3 78.0 - - - +
106C TYR* 1.3 57.6 + - - +
107C GLY 3.4 0.5 + - - -
242D ARG* 4.2 3.8 - - - +
245D ALA* 3.3 17.6 - - - +
246D VAL* 3.9 10.7 - - - +
251D PHE* 3.3 30.5 - - + -
292D PHE* 3.9 23.8 - - + -
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Residues in contact with TYR 106 (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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36C PRO 4.6 2.8 + - - -
37C ALA* 3.8 19.6 - - - +
74C ILE* 3.8 25.0 - - + +
77C ALA* 3.3 36.2 - - + +
78C MET* 3.4 23.8 - - + +
81C ALA* 4.2 7.8 - - - +
102C ALA* 3.3 23.1 + - + -
103C MET 3.0 3.0 + - - +
105C ALA* 1.3 77.5 - - + +
107C GLY* 1.3 59.8 + - - +
108C ALA 3.5 0.4 + - - -
245D ALA* 3.6 27.5 - - + +
246D VAL* 4.0 11.7 - - - +
249D GLY 2.9 28.0 + - - -
251D PHE* 3.3 35.7 + + + +
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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