Contacts of the helix formed by residues 8 - 21 (chain B) in PDB entry 3SE3
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 SER 8 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9B LEU* 1.3 66.1 + - - -
10B GLY* 4.0 6.5 - - - +
11B SER* 3.7 26.7 + - - +
12B ARG* 3.9 10.6 + - - +
155B THR* 5.3 3.4 - - - +
188C SER* 5.5 1.7 + - - -
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Residues in contact with LEU 9 (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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8B SER* 1.3 79.5 - - - +
10B GLY* 1.3 63.1 + - - +
11B SER 3.4 0.2 - - - -
12B ARG* 3.7 5.4 + - - +
13B ARG* 3.1 28.1 + - + +
190C GLU* 4.2 25.4 - - - +
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Residues in contact with GLY 10 (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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8B SER* 3.2 5.5 - - - +
9B LEU* 1.3 79.9 - - - +
11B SER* 1.3 49.9 + - - +
13B ARG* 3.6 0.7 - - - +
14B THR* 2.5 44.7 + - - -
87B GLU* 4.1 14.3 - - - +
91B GLN* 3.8 17.9 - - - -
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Residues in contact with SER 11 (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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8B SER 3.7 18.2 + - - +
9B LEU 3.4 0.4 - - - -
10B GLY* 1.3 70.8 - - - +
12B ARG* 1.3 68.0 + - - +
14B THR* 3.7 0.2 - - - -
15B LEU* 2.9 34.2 + - - +
91B GLN* 4.4 1.9 + - - +
151B PHE* 3.7 23.6 - - - -
155B THR* 3.1 37.7 + - - +
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Residues in contact with ARG 12 (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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8B SER 3.9 9.1 + - - +
9B LEU* 3.7 6.2 + - - +
10B GLY 3.5 0.4 - - - -
11B SER* 1.3 81.1 - - - +
13B ARG* 1.3 61.3 + - - +
15B LEU* 4.1 4.9 - - - +
16B MET* 3.3 24.2 + - - +
103C ILE* 5.4 2.9 - - - +
188C SER* 4.3 20.6 - - - +
190C GLU* 4.9 13.5 - - + -
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Residues in contact with ARG 13 (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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9B LEU* 3.1 21.1 + - + +
10B GLY 3.6 1.8 - - - +
12B ARG* 1.3 76.2 - - - +
14B THR* 1.3 58.8 + - - +
16B MET* 4.2 11.6 - - - +
17B LEU* 3.6 23.9 + - - +
87B GLU* 4.5 18.9 - - - +
190C GLU* 6.5 1.3 - - + -
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Residues in contact with THR 14 (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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10B GLY 2.5 27.6 + - - -
11B SER 3.7 3.1 - - - -
13B ARG* 1.3 72.2 - - - +
15B LEU* 1.3 67.0 + - - +
16B MET 3.2 0.9 - - - -
17B LEU* 3.0 16.2 + - - +
18B LEU* 3.1 16.9 + - + +
84B PHE* 3.6 27.8 - - + -
87B GLU* 3.3 15.6 - - + +
88B LEU* 5.0 4.9 - - + -
91B GLN* 3.1 17.5 + - - +
151B PHE* 4.1 24.5 - - + -
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Residues in contact with LEU 15 (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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11B SER* 2.9 23.5 + - - +
12B ARG* 4.1 4.7 - - - +
14B THR* 1.3 76.6 - - - +
16B MET* 1.3 53.9 + - - +
18B LEU* 3.0 7.5 + - + -
19B ALA 2.6 33.1 + - - -
148B MET* 3.3 48.4 - - + +
151B PHE* 3.6 26.7 - - + -
152B SER* 4.0 20.0 - - - -
155B THR* 6.3 0.2 - - - -
100C TRP* 4.2 15.0 - - + +
102C ALA* 5.7 3.4 - - + -
103C ILE* 4.0 14.6 - - + -
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Residues in contact with MET 16 (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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12B ARG 3.3 16.4 + - - +
13B ARG* 4.2 10.5 - - - +
15B LEU* 1.3 78.1 - - - +
17B LEU* 1.3 53.2 + - + +
19B ALA* 3.2 2.7 + - + +
20B GLN* 2.7 61.2 + - + +
103C ILE* 3.9 31.0 - - + +
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Residues in contact with LEU 17 (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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13B ARG 3.6 16.2 - - - +
14B THR* 3.0 8.6 + - - +
16B MET* 1.3 76.8 - - + +
18B LEU* 1.3 67.5 + - - +
20B GLN* 3.0 13.4 + - - +
21B MET* 3.0 29.1 + - - +
80B LEU* 3.8 24.5 - - + +
83B LYS* 3.3 27.4 - - + +
84B PHE* 3.3 45.3 - - + +
87B GLU* 4.2 9.0 - - + -
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Residues in contact with LEU 18 (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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14B THR* 3.1 14.0 + - + +
15B LEU* 3.0 15.4 + - + +
17B LEU* 1.3 76.1 - - - +
19B ALA* 1.3 63.0 + - - +
21B MET* 3.2 27.3 + - - +
67B PHE* 4.6 14.4 - - + -
84B PHE* 3.7 37.2 - - + -
144B ARG* 3.3 35.6 + - + +
147B ILE* 4.4 16.8 - - + -
148B MET* 3.6 28.5 - - + -
151B PHE* 5.3 3.8 - - + -
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Residues in contact with ALA 19 (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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15B LEU 2.6 19.7 + - - +
16B MET* 3.3 5.6 - - + +
18B LEU* 1.3 75.3 - - - +
20B GLN* 1.3 63.0 + - + +
21B MET 3.2 0.5 + - - -
22B ARG* 3.5 16.1 + - - +
144B ARG* 4.2 3.0 + - - +
148B MET* 3.3 20.6 - - + +
100C TRP* 5.9 1.6 - - + -
103C ILE* 3.8 18.4 - - + -
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Residues in contact with GLN 20 (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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16B MET* 2.7 44.3 + - + +
17B LEU* 3.0 14.5 + - - +
19B ALA* 1.3 76.4 - - + +
21B MET* 1.3 58.5 + - - +
22B ARG* 2.9 11.3 + - - +
80B LEU* 3.3 34.3 - - + +
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Residues in contact with MET 21 (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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17B LEU 3.0 21.9 + - - +
18B LEU* 3.2 32.6 + - + +
20B GLN* 1.3 76.8 - - - +
22B ARG* 1.3 63.1 + - - +
23B ARG* 3.2 2.1 + - - +
67B PHE* 5.0 7.0 - - + -
76B TRP* 3.1 51.9 - - + -
77B ASP* 5.4 3.6 + - - +
80B LEU* 3.6 25.8 - - + +
81B LEU* 3.5 37.0 - - + +
84B PHE* 4.4 17.0 - - + -
144B ARG* 4.0 4.9 - - - -
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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