Contacts of the helix formed by residues 92 - 103 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A ARG* 3.4 39.0 - - - +
87B TYR 4.5 1.1 - - - +
88B GLN* 2.8 32.9 + - - +
89B ARG* 3.1 22.2 + - - +
91B ALA* 1.3 77.2 - - - +
93B PRO* 1.4 73.4 - - + +
94B GLU* 4.7 2.5 - - + +
95B GLN* 3.0 41.4 + - + +
96B ILE* 3.2 6.8 + - - +
113B TYR* 4.8 1.6 - - + -
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Residues in contact with PRO 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A TYR* 3.7 24.2 - - + -
273A ASP* 3.5 24.0 - - + +
277A ARG* 4.5 2.7 - - - +
91B ALA 3.6 1.3 - - - +
92B LYS* 1.4 83.5 - - + +
94B GLU* 1.4 56.3 + - - +
96B ILE* 3.5 3.3 + - + +
97B GLN* 3.1 31.9 + - - +
112B LYS* 4.1 19.5 - - + -
113B TYR 3.2 24.7 - - - +
114B TRP* 3.6 29.8 - - + -
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Residues in contact with GLU 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A PRO* 3.9 14.4 - - - +
270A TYR* 3.7 21.3 + - + +
273A ASP* 5.1 2.6 + - - +
274A SER* 3.3 23.3 + - - +
277A ARG* 5.6 9.9 - - - +
278A TYR* 3.0 39.8 + - - -
288A LYS* 4.5 9.4 + - - +
92B LYS* 3.3 2.6 - - + +
93B PRO* 1.4 76.1 - - - +
95B GLN* 1.4 59.1 + - - +
97B GLN* 3.9 0.6 - - - +
98B LYS* 3.0 34.8 + - + +
101B ARG* 5.6 3.1 + - - +
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Residues in contact with GLN 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ARG 2.9 29.0 + - - +
90B ALA 3.3 9.6 - - - -
92B LYS* 3.2 50.0 + - + +
94B GLU* 1.4 77.0 - - - +
96B ILE* 1.3 59.1 + - - +
98B LYS* 3.7 5.9 + - - +
99B TRP* 3.4 21.5 + - - +
167B TYR* 3.5 12.7 + - - +
171B HIS* 3.5 25.3 + - - +
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Residues in contact with ILE 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ALA* 3.8 31.0 - - + +
92B LYS 3.2 5.1 + - - +
93B PRO 3.8 7.0 - - - +
95B GLN* 1.3 74.2 - - - +
97B GLN* 1.4 58.4 + - - +
99B TRP* 3.2 4.9 + - - +
100B ILE* 2.9 46.0 + - + +
108B LEU* 3.9 19.5 - - + +
110B VAL* 3.8 19.5 - - + +
111B PRO 4.1 0.4 - - - +
112B LYS* 3.8 38.4 - - + +
167B TYR* 3.6 26.0 - - + +
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Residues in contact with GLN 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A ASP 5.7 0.2 + - - -
264A ASN* 3.3 29.4 + - - +
270A TYR* 3.5 31.9 - - + +
93B PRO 3.1 19.9 + - - +
94B GLU* 4.0 1.8 - - + +
96B ILE* 1.4 71.7 - - - +
98B LYS* 1.4 65.2 + - - +
100B ILE* 3.4 26.2 + - - +
101B ARG* 3.0 34.7 + - - +
112B LYS* 3.5 24.5 + - - -
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Residues in contact with LYS 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A LYS* 5.4 6.1 - - - +
94B GLU* 3.0 22.7 + - + +
95B GLN* 3.9 6.5 - - - +
97B GLN* 1.4 75.9 - - - +
99B TRP* 1.4 54.0 + - - +
101B ARG* 3.5 27.5 + - - +
102B THR* 2.8 44.5 + - - +
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Residues in contact with TRP 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B GLN 3.4 11.0 + - - +
96B ILE 3.2 8.8 + - - +
98B LYS* 1.4 76.4 - - - +
100B ILE* 1.4 59.1 + - - +
102B THR* 4.6 4.0 - - - -
103B ARG* 2.9 88.0 + - + +
105B LEU* 3.7 22.4 - - + +
108B LEU* 4.2 8.7 - - + +
163B ASP* 4.7 2.0 + - - +
166B GLU* 4.1 6.3 - - + -
167B TYR* 3.3 49.2 - + + +
170B GLU* 3.9 24.9 - - + -
171B HIS* 3.9 19.3 - + - -
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Residues in contact with ILE 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ILE* 2.9 38.9 + - + +
97B GLN* 3.4 30.3 + - - +
99B TRP* 1.4 72.6 - - - +
101B ARG* 1.3 59.7 + - - +
104B LYS* 3.0 9.9 + - - -
105B LEU* 2.9 55.2 + - + +
106B LYS 4.6 7.4 - - - +
107B TYR* 4.0 7.4 - - - +
108B LEU* 3.7 34.1 - - + +
112B LYS* 5.0 2.9 - - - +
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Residues in contact with ARG 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A PRO 5.7 2.4 + - - -
263A ASP* 4.9 19.7 - - - +
264A ASN* 5.3 1.2 - - - +
270A TYR* 5.2 3.8 + - - -
288A LYS* 4.0 20.6 - - - +
94B GLU* 6.1 3.2 - - - +
97B GLN* 3.0 38.0 + - - +
98B LYS* 3.5 31.6 + - - +
100B ILE* 1.3 77.4 - - - +
102B THR* 1.4 63.8 + - - +
104B LYS* 3.3 14.6 + - - +
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Residues in contact with THR 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LYS* 2.8 33.5 + - - +
99B TRP* 4.0 4.7 - - - -
101B ARG* 1.4 76.2 + - - +
103B ARG* 1.4 70.9 + - - +
104B LYS* 3.5 2.8 + - - +
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Residues in contact with ARG 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B TRP* 2.9 74.1 + - + +
102B THR* 1.4 83.0 - - - +
104B LYS* 1.4 67.6 + - - +
105B LEU* 3.4 24.1 + - + +
166B GLU* 3.2 35.0 + - - +
170B GLU* 4.7 5.9 + - - +
321B ARG* 5.3 2.2 - - - +
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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