Contacts of the helix formed by residues 92 - 104 (chain D) in PDB entry 3OP5
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 LYS 92 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87D TYR 4.4 1.6 - - - +
88D GLN* 2.8 33.3 + - - +
89D ARG* 3.3 21.6 + - - +
91D ALA* 1.3 76.4 - - - +
93D PRO* 1.4 75.1 - - + +
94D GLU* 3.2 4.7 - - + +
95D GLN* 3.0 41.7 + - + +
96D ILE* 3.2 6.6 + - - +
113D TYR* 5.5 6.3 - - + -
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Residues in contact with PRO 93 (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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91D ALA 3.6 3.6 - - - +
92D LYS* 1.4 83.2 - - + +
94D GLU* 1.4 55.8 + - - +
96D ILE* 3.5 8.9 + - + +
97D GLN* 3.1 36.1 + - + +
112D LYS* 3.8 39.0 - - + +
113D TYR* 3.8 22.4 - - + +
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Residues in contact with GLU 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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92D LYS* 3.2 4.6 - - + +
93D PRO* 1.4 75.3 - - - +
95D GLN* 1.3 59.7 + - - +
97D GLN* 4.0 5.8 - - - +
98D LYS* 3.1 30.8 + - - +
101D ARG* 5.5 0.2 + - - -
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Residues in contact with GLN 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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89D ARG 2.9 23.9 + - - +
90D ALA 3.3 13.5 - - - -
92D LYS* 3.0 50.0 + - + +
94D GLU* 1.3 79.6 - - - +
96D ILE* 1.3 61.0 + - - +
98D LYS* 3.7 5.6 + - - +
99D TRP* 3.4 20.4 + - - +
167D TYR* 3.6 13.2 + - - +
171D HIS* 3.5 25.3 + - - +
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Residues in contact with ILE 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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91D ALA* 3.7 32.1 - - + +
92D LYS 3.2 6.5 + - - +
93D PRO* 3.8 9.6 - - + +
95D GLN* 1.3 73.1 - - - +
97D GLN* 1.4 64.2 + - - +
99D TRP* 3.2 4.9 + - - +
100D ILE* 2.9 46.0 + - + +
108D LEU* 3.9 18.6 - - + +
110D VAL* 3.9 31.2 - - + +
111D PRO 4.0 4.7 - - - +
112D LYS* 5.0 3.6 - - - -
167D TYR* 3.6 26.2 - - + +
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Residues in contact with GLN 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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93D PRO* 3.1 22.6 + - + +
94D GLU* 4.2 5.6 - - - +
95D GLN 3.5 0.2 - - - -
96D ILE* 1.4 75.7 - - - +
98D LYS* 1.4 63.6 + - - +
100D ILE* 3.4 29.4 + - - +
101D ARG* 3.1 29.3 + - - +
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Residues in contact with LYS 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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94D GLU 3.1 20.3 + - - +
95D GLN* 3.9 6.5 - - - +
96D ILE 3.3 0.2 - - - -
97D GLN* 1.4 74.0 - - - +
99D TRP* 1.3 52.1 + - - +
101D ARG* 3.5 30.9 + - - +
102D THR* 2.7 48.3 + - + +
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Residues in contact with TRP 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 GLN 3.4 10.5 + - - +
96D ILE 3.2 9.1 + - - +
98D LYS* 1.3 76.7 - - - +
100D ILE* 1.4 59.6 + - - +
102D THR* 3.1 6.5 + - - -
103D ARG* 2.9 90.5 + - + +
105D LEU* 3.7 21.6 - - + +
108D LEU* 4.2 8.5 - - + +
163D ASP 4.6 2.8 + - - -
166D GLU* 4.2 16.2 - - + -
167D TYR* 3.3 48.8 - + + +
170D GLU* 3.9 29.2 - - + -
171D HIS* 3.9 20.2 - + - -
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Residues in contact with ILE 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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96D ILE* 2.9 38.2 + - + +
97D GLN* 3.4 31.4 + - - +
99D TRP* 1.4 74.3 - - - +
101D ARG* 1.3 57.9 + - - +
104D LYS* 3.0 9.2 + - - -
105D LEU* 2.9 54.9 + - - +
106D LYS 4.7 7.4 - - - +
107D TYR* 4.1 6.3 - - - +
108D LEU* 3.7 35.2 - - + +
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Residues in contact with ARG 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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319A ASN* 4.9 12.3 - - - +
97D GLN* 3.1 17.8 + - - +
98D LYS* 3.5 39.4 - - - +
100D ILE* 1.3 78.3 - - - +
102D THR* 1.3 72.0 + - - +
104D LYS* 3.2 18.8 + - - +
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Residues in contact with THR 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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308A LEU* 3.6 37.6 - - + +
98D LYS* 2.7 36.2 + - + +
99D TRP* 3.1 13.3 + - - -
101D ARG* 1.3 84.9 - - - +
103D ARG* 1.3 74.1 + - - +
104D LYS* 3.3 12.5 + - - +
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Residues in contact with ARG 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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304A GLU* 5.0 9.9 + - - -
308A LEU* 3.5 37.4 - - + +
99D TRP* 2.9 76.1 + - + +
102D THR* 1.3 92.1 + - - +
104D LYS* 1.4 74.9 + - - +
105D LEU* 3.3 25.3 + - + +
166D GLU* 5.8 2.3 + - - +
170D GLU* 5.5 2.4 + - - +
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Residues in contact with LYS 104 (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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308A LEU* 3.7 15.1 + - - -
310A ASP* 3.3 27.7 + - - -
313A GLU* 3.1 36.0 + - - +
100D ILE 3.0 7.8 + - - -
101D ARG 3.2 13.3 + - - +
102D THR 4.0 11.0 - - - +
103D ARG* 1.4 83.4 - - - +
105D LEU* 1.3 61.9 + - - +
106D LYS 4.2 0.3 + - - -
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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