Contacts of the helix formed by residues 93 - 103 (chain C) in PDB entry 2H5X
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 ASP 93 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33C ALA* 4.5 18.7 - - - +
89C LEU 4.2 5.9 - - - +
90C ALA 5.7 0.9 - - - +
91C VAL 5.4 0.7 - - - +
92C HIS* 1.3 73.3 - - - +
94C ALA* 1.3 68.3 - - - +
95C PRO* 3.0 15.4 - - + -
96C ALA* 3.0 10.6 + - + +
97C LEU* 2.8 20.6 + - - +
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Residues in contact with ALA 94 (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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66C GLU* 3.0 27.6 - - - +
67C THR* 3.7 27.4 - - + +
70C LEU* 3.8 18.0 - - + +
89C LEU* 4.4 7.4 - - - +
92C HIS 3.7 1.2 + - - -
93C ASP* 1.3 69.9 - - - +
95C PRO* 1.3 70.3 - - + +
97C LEU* 3.5 0.4 + - - -
98C ARG* 2.9 31.8 + - - +
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Residues in contact with PRO 95 (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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66C GLU* 4.6 6.3 - - - +
93C ASP* 3.1 17.3 - - + -
94C ALA* 1.3 96.9 - - + +
96C ALA* 1.3 64.0 + - - +
98C ARG* 3.0 26.9 + - - +
99C GLN* 3.2 5.9 + - - +
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Residues in contact with ALA 96 (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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92C HIS* 4.6 10.5 - - + -
93C ASP* 3.0 17.3 + - + +
95C PRO* 1.3 76.7 - - + +
97C LEU* 1.3 59.2 + - - +
99C GLN* 2.6 32.5 + - - +
100C VAL* 2.8 16.8 + - + +
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Residues in contact with LEU 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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70C LEU* 4.5 6.7 - - + -
74C LEU* 4.3 21.5 - - + -
88C ALA* 4.3 17.5 - - + +
89C LEU* 3.6 26.5 - - + -
92C HIS* 3.9 24.5 - - + +
93C ASP 2.8 19.9 + - - +
94C ALA* 3.9 4.7 - - - +
96C ALA* 1.3 72.6 - - - +
98C ARG* 1.3 63.5 + - - +
100C VAL* 3.3 6.0 + - + -
101C LEU* 3.0 34.3 + - + +
109C LEU* 3.8 28.7 - - + -
112C VAL* 6.2 0.2 - - + -
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Residues in contact with ARG 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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66C GLU* 2.7 53.1 + - - +
70C LEU* 4.0 20.2 - - + +
94C ALA* 2.9 33.4 + - - +
95C PRO* 3.0 20.5 + - - +
96C ALA 3.0 0.6 - - - -
97C LEU* 1.3 75.6 - - - +
99C GLN* 1.3 57.3 + - - +
101C LEU* 3.3 3.4 + - - +
102C ALA* 2.8 31.4 + - - +
131C VAL* 2.9 50.9 + - + +
132C GLY* 4.6 4.5 - - - +
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Residues in contact with GLN 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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95C PRO 3.2 5.0 + - - +
96C ALA* 2.6 24.2 + - - +
98C ARG* 1.3 73.1 - - - +
100C VAL* 1.3 56.6 + - + +
101C LEU 3.0 0.3 + - - -
102C ALA* 3.1 8.0 + - - +
103C ASP* 2.7 65.0 + - + +
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Residues in contact with VAL 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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92C HIS* 4.3 17.7 - - + +
96C ALA* 2.8 19.2 + - + +
97C LEU* 3.5 9.2 - - + +
99C GLN* 1.3 75.7 - - + +
101C LEU* 1.3 58.9 + - - +
104C GLY* 3.0 6.2 + - - -
105C ASN* 2.8 54.3 + - + +
108C ALA* 4.0 16.8 - - + -
109C LEU* 3.3 38.8 - - + +
124C VAL* 4.6 1.2 - - - +
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Residues in contact with LEU 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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70C LEU* 4.9 7.0 - - + -
74C LEU* 4.5 8.5 - - + -
97C LEU* 3.0 34.8 + - + +
98C ARG* 3.6 3.8 - - - +
99C GLN 3.0 0.4 - - - -
100C VAL* 1.3 76.2 - - - +
102C ALA* 1.3 63.7 + - - +
104C GLY* 3.0 10.0 + - - -
109C LEU* 3.7 28.3 - - + -
123C MET* 4.4 12.1 - - + +
124C VAL* 3.8 12.7 - - - +
127C LEU* 3.7 40.6 - - + -
128C ARG* 3.0 22.0 + - - +
131C VAL* 4.2 19.3 - - + -
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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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98C ARG 2.8 20.4 + - - +
99C GLN* 3.9 11.0 - - - +
101C LEU* 1.3 72.4 - - - +
103C ASP* 1.3 63.4 + - - +
128C ARG* 3.1 28.3 + - - +
131C VAL* 3.9 17.2 - - + +
132C GLY 6.0 2.2 - - - +
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Residues in contact with ASP 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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99C GLN* 2.7 52.2 + - - +
102C ALA* 1.3 75.2 - - - +
104C GLY* 1.3 67.1 + - - +
105C ASN* 2.9 11.6 + - + +
128C ARG* 3.1 10.2 + - - +
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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