Contacts of the helix formed by residues 93 - 103 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33D ALA* 5.1 13.6 - - - +
67D THR* 5.9 1.0 - - - +
89D LEU 3.8 6.1 + - - +
90D ALA 5.3 0.2 + - - -
91D VAL 4.3 0.4 + - - -
92D HIS* 1.3 73.2 - - - +
94D ALA* 1.3 66.9 + - - +
95D PRO* 3.2 19.5 - - + +
96D ALA* 3.0 12.2 + - + +
97D LEU* 2.7 30.0 + - - +
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Residues in contact with ALA 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D THR* 4.0 32.1 - - + +
70D LEU* 3.9 22.6 - - + +
89D LEU* 4.1 8.1 - - + +
92D HIS 3.6 1.0 + - - -
93D ASP* 1.3 76.0 + - - +
95D PRO* 1.3 65.2 - - + +
97D LEU* 3.8 1.3 - - - +
98D ARG* 2.9 43.7 + - - +
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Residues in contact with PRO 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D ASP* 3.3 21.5 - - + +
94D ALA* 1.3 97.2 - - + +
96D ALA* 1.3 60.8 + - - +
98D ARG* 3.4 12.7 - - - +
99D GLN* 3.3 19.1 + - - +
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Residues in contact with ALA 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D HIS* 4.7 8.1 - - + +
93D ASP* 3.0 18.4 + - + +
95D PRO* 1.3 76.5 - - - +
97D LEU* 1.3 67.4 + - - +
98D ARG 3.0 1.6 - - - -
99D GLN* 2.8 44.6 + - - +
100D VAL* 2.8 10.6 + - + +
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Residues in contact with LEU 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D LEU* 4.3 7.6 - - + -
74D LEU* 4.1 23.8 - - + -
88D ALA* 4.4 7.4 - - + +
89D LEU* 3.4 34.3 - - + +
92D HIS* 3.8 25.0 - - + +
93D ASP 2.7 20.9 + - - +
94D ALA* 3.8 4.3 - - - +
96D ALA* 1.3 71.9 - - - +
98D ARG* 1.3 62.2 + - - +
100D VAL* 3.4 4.7 + - + +
101D LEU* 3.0 48.4 + - + +
109D LEU* 4.0 13.0 - - + -
123D MET* 6.5 0.2 - - - -
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Residues in contact with ARG 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D GLU* 3.9 21.6 + - - +
67D THR* 5.3 0.4 - - - +
69D ASP* 5.9 0.4 - - - +
70D LEU* 3.8 41.7 - - + +
94D ALA* 2.9 33.6 + - - +
95D PRO* 3.4 11.9 - - - +
97D LEU* 1.3 78.5 - - - +
99D GLN* 1.3 58.5 + - - +
101D LEU* 3.4 3.3 + - - +
102D ALA* 2.8 30.6 + - - +
131D VAL* 4.0 22.8 - - + +
132D GLY* 3.7 33.2 - - - +
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Residues in contact with GLN 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D PRO 3.3 7.4 + - - +
96D ALA* 2.8 39.5 + - - +
98D ARG* 1.3 76.4 - - - +
100D VAL* 1.3 70.3 + - + +
101D LEU 3.0 1.8 - - - -
102D ALA* 4.3 5.8 - - - -
103D ASP* 2.5 45.3 + - + +
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Residues in contact with VAL 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D HIS* 4.5 12.3 - - + +
96D ALA* 2.8 19.2 + - + +
97D LEU* 3.7 10.5 - - - +
99D GLN* 1.3 91.2 - - + +
101D LEU* 1.3 59.2 + - + +
103D ASP* 4.6 0.7 - - - -
104D GLY 2.9 5.0 + - - -
105D ASN* 2.7 60.7 + - + +
108D ALA* 3.4 25.8 - - + -
109D LEU* 3.6 21.3 - - + +
124D VAL* 4.8 0.5 - - - +
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Residues in contact with LEU 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D LEU* 5.4 2.9 - - + -
74D LEU* 4.4 8.3 - - + -
97D LEU* 3.0 33.9 + - + +
98D ARG* 3.7 3.4 - - - +
99D GLN 3.0 0.4 - - - -
100D VAL* 1.3 75.1 - - - +
102D ALA* 1.3 59.5 + - - +
104D GLY* 2.6 25.8 + - - -
109D LEU* 3.2 48.0 - - + -
123D MET* 4.5 17.5 - - + +
124D VAL* 3.8 12.9 - - + +
127D LEU* 3.9 28.7 - - + -
128D ARG* 4.2 8.3 - - - +
131D VAL* 4.6 16.4 - - + -
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Residues in contact with ALA 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D ARG 2.8 21.3 + - - +
99D GLN* 3.8 5.6 - - - +
101D LEU* 1.3 74.1 - - - +
103D ASP* 1.3 62.6 + - - +
104D GLY 3.3 0.3 + - - -
128D ARG* 3.4 35.7 + - - +
131D VAL* 3.9 15.1 - - + +
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Residues in contact with ASP 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D GLN* 2.5 30.6 + - + +
100D VAL* 4.2 3.6 - - - +
102D ALA* 1.3 74.9 - - - +
104D GLY* 1.3 62.7 + - - +
105D ASN* 3.5 6.3 + - + +
128D ARG* 4.7 5.2 + - - -
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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