Contacts of the helix formed by residues 93 - 101 (chain B) in PDB entry 3T0E
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 GLN 93 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ARG* 3.1 34.1 + - - +
10B PRO* 5.9 0.8 - - - +
89B TYR* 3.7 31.6 + - + +
90B TRP* 2.9 43.0 + - - +
91B ASN 4.6 1.6 - - - -
92B SER* 1.3 79.2 - - - +
94B LYS* 1.3 69.7 + - - +
95B ASP* 3.5 10.7 + - - +
96B LEU* 4.4 5.6 - - + -
97B LEU* 3.6 14.2 + - - +
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Residues in contact with LYS 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ASN 5.7 0.7 - - - -
92B SER 3.5 5.5 + - - -
93B GLN* 1.3 73.2 - - - +
95B ASP* 1.3 69.4 + - - +
97B LEU* 3.2 11.5 + - - +
98B GLU* 3.5 8.5 + - - +
101B ARG* 5.9 0.2 + - - -
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Residues in contact with ASP 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ARG* 3.6 15.7 + - - -
93B GLN* 3.9 12.6 - - - +
94B LYS* 1.3 74.8 + - - +
96B LEU* 1.3 71.8 + - - -
98B GLU* 2.5 40.3 + - - +
99B GLN* 3.3 15.2 + - - +
48C HIS* 6.3 3.6 - - + -
102D PRO* 3.2 31.2 - - - +
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Residues in contact with LEU 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B GLY 5.4 4.0 - - - +
8B GLN 6.4 0.2 - - - -
9B ARG* 3.4 52.3 - - + +
76B TYR* 4.0 13.0 - - + +
90B TRP* 4.0 38.4 - - + +
93B GLN* 4.2 9.0 - - + +
94B LYS 3.4 0.4 - - - -
95B ASP* 1.3 84.2 + - - +
97B LEU* 1.3 58.2 + - + +
99B GLN* 2.9 29.9 + - + +
100B LYS* 3.0 36.3 + - + +
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Residues in contact with LEU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B PHE* 4.2 8.3 - - + -
74B GLY 3.0 28.5 - - - +
75B GLU* 3.8 11.9 - - + -
76B TYR* 5.3 4.9 - - + +
90B TRP 5.1 1.1 - - - +
91B ASN* 3.6 46.4 - - + +
93B GLN 3.6 5.3 + - - +
94B LYS* 3.2 11.8 + - - +
95B ASP 2.9 0.8 + - - -
96B LEU* 1.3 81.0 - - - +
98B GLU* 1.3 57.0 + - - +
100B LYS* 4.7 3.8 - - - +
101B ARG* 3.0 62.7 + - + +
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Residues in contact with GLU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B LYS 3.5 5.0 + - - +
95B ASP* 2.5 24.0 + - - +
97B LEU* 1.3 73.2 - - - +
99B GLN* 1.3 60.1 + - + +
101B ARG* 4.1 14.6 - - + +
102B ALA* 3.8 16.1 + - - +
31C TYR* 5.0 1.0 + - - -
48C HIS* 5.2 6.9 + - - -
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Residues in contact with GLN 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B GLU* 6.0 2.2 - - - +
9B ARG* 3.7 14.8 + - - +
95B ASP* 4.0 19.9 + - - +
96B LEU* 2.9 16.5 + - + +
98B GLU* 1.3 77.5 - - + +
100B LYS* 1.3 59.2 + - + +
101B ARG 3.0 0.9 - - - -
102B ALA* 2.8 26.2 + - - +
103B ALA* 3.2 9.0 + - - -
106B THR* 4.5 3.5 + - - -
31C TYR* 4.2 30.4 + - + +
48C HIS* 6.1 1.4 + - - -
99D TYR 4.9 0.2 - - - +
100D ASN* 3.0 44.7 + - - +
102D PRO* 5.4 1.2 - - - +
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Residues in contact with LYS 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B GLU* 3.2 27.8 + - - +
7B GLY 3.3 20.4 + - - -
8B GLN* 5.8 0.2 - - - +
42B HIS* 4.0 4.8 + - - -
55B PHE* 4.4 10.3 - - + -
57B ASP* 2.1 37.7 + - + +
59B TYR* 4.6 1.7 + - - -
69B PHE* 3.2 35.0 - - + -
71B SER* 5.7 0.7 - - - -
76B TYR* 3.1 28.0 - - + +
96B LEU* 3.0 29.3 + - + +
97B LEU* 4.4 1.6 - - - +
99B GLN* 1.3 80.0 - - + +
101B ARG* 1.3 61.1 + - - +
103B ALA* 3.0 22.2 - - - +
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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
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69B PHE* 4.0 4.9 - - + -
71B SER* 5.7 1.0 + - - -
74B GLY* 3.0 37.4 + - - +
75B GLU* 4.9 6.5 + - - +
97B LEU* 3.0 50.9 + - + +
98B GLU* 4.2 12.6 - - + +
99B GLN 3.0 0.2 - - - -
100B LYS* 1.3 76.7 - - - +
102B ALA* 1.3 60.7 + - - +
103B ALA* 3.2 1.1 + - - +
104B VAL* 4.9 6.9 + - - +
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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