Contacts of the helix formed by residues 9 - 23 (chain B) in PDB entry 3SE4
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 HIS 9 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B LEU* 3.8 11.4 - - + +
6B PRO* 3.5 20.2 - - + +
7B GLN 3.1 3.8 + - - -
8B ASN* 1.3 74.1 - - - +
10B GLY* 1.3 64.4 + - - +
11B LEU 3.0 1.3 - - - -
12B LEU* 2.8 23.0 + - + -
13B SER* 3.0 16.4 + - - -
59B LEU* 4.8 17.9 - - + -
63B LEU* 5.8 0.9 - - + -
94B GLN* 3.6 34.0 + - + +
97B HIS* 2.6 43.0 + + - -
98B LEU* 5.3 6.7 - - + +
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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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7B GLN 4.4 4.0 + - - -
9B HIS* 1.3 78.1 + - - +
11B LEU* 1.3 58.0 + - - +
13B SER* 3.7 4.9 + - - -
14B ARG* 3.3 23.4 + - - +
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Residues in contact with LEU 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ASN* 4.2 22.8 - - + +
9B HIS 3.0 1.6 - - - +
10B GLY* 1.3 76.6 - - - +
12B LEU* 1.3 59.6 + - + +
14B ARG* 3.9 6.0 - - - +
15B ASN* 3.3 30.5 + - - +
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Residues in contact with LEU 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B PRO* 5.1 0.7 - - + -
8B ASN 3.6 15.7 - - - +
9B HIS* 2.8 17.9 + - + +
11B LEU* 1.3 77.5 - - + +
13B SER* 1.3 65.0 + - - +
14B ARG 3.0 1.3 - - - -
15B ASN* 3.2 19.9 + - + +
16B THR 3.4 5.2 + - - -
90B GLY* 4.9 8.1 - - - +
93B GLN* 2.9 35.2 - - + +
94B GLN* 3.0 31.8 + - + -
97B HIS* 3.4 33.9 - - + -
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Residues in contact with SER 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B HIS* 3.0 20.4 + - - -
10B GLY* 4.3 5.4 - - - -
12B LEU* 1.3 77.0 - - - +
14B ARG* 1.3 64.0 + - - +
16B THR* 3.5 11.0 + - - -
17B LEU* 3.6 16.6 + - - +
59B LEU* 5.8 4.2 - - - +
63B LEU* 5.8 1.4 - - - +
94B GLN* 3.6 20.0 + - - +
154B LEU* 5.6 5.4 - - - +
158B THR* 3.2 27.4 + - - -
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Residues in contact with ARG 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 3.3 16.9 + - - +
11B LEU* 3.9 7.4 - - - +
12B LEU 3.0 0.4 - - - -
13B SER* 1.3 75.4 - - - +
15B ASN* 1.3 55.9 + - - +
16B THR 3.0 3.6 - - - -
17B LEU* 2.7 38.6 + - - +
18B VAL* 3.0 16.9 + - + +
155B PHE* 5.0 5.3 - - - -
158B THR* 6.0 1.3 - - - +
102C ALA* 3.1 29.7 + - - +
103C ILE* 4.1 17.1 + - - +
187C HIS* 3.8 13.5 + - - -
188C SER* 4.2 14.0 + - - +
190C GLU* 2.8 46.1 + - + +
191C GLN* 3.4 28.3 + - - +
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Residues in contact with ASN 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 LEU* 3.3 18.2 + - - +
12B LEU* 3.2 14.2 + - + +
14B ARG* 1.3 74.8 - - - +
16B THR* 1.3 60.4 + - - +
18B VAL* 3.9 9.9 - - - +
19B LEU* 3.2 31.1 + - + +
90B GLY* 6.5 1.1 - - - -
190C GLU* 3.8 17.2 - - - +
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Residues in contact with THR 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 LEU 3.4 1.7 + - - -
13B SER* 3.7 10.1 - - - -
14B ARG 3.0 1.0 - - - -
15B ASN* 1.3 75.3 - - - +
17B LEU* 1.3 63.0 + - - +
19B LEU* 3.0 7.8 + - - +
20B LEU* 2.8 32.4 + - + +
63B LEU* 5.3 1.3 - - + -
66B ILE* 5.5 0.9 - - + -
87B LEU* 3.9 21.0 + - + +
90B GLY* 4.1 9.0 + - - -
91B LEU* 4.1 19.8 - - + +
94B GLN* 2.9 26.7 + - - -
154B LEU* 3.9 23.6 - - + -
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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 SER 3.6 12.1 + - - +
14B ARG* 2.7 23.8 + - - +
16B THR* 1.3 73.1 - - - +
18B VAL* 1.3 57.3 + - + +
20B LEU* 3.4 6.1 + - + +
21B HIS* 2.9 29.0 + - - +
151B MET* 4.0 21.7 - - + +
154B LEU* 3.4 38.6 - - + -
155B PHE* 3.7 39.9 - - + +
158B THR* 4.0 26.2 - - + +
103C ILE* 4.5 6.1 - - + +
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Residues in contact with VAL 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 ARG* 3.0 33.1 + - + +
15B ASN* 3.9 8.5 - - - +
17B LEU* 1.3 75.3 - - + +
19B LEU* 1.3 58.0 + - + +
21B HIS* 3.3 7.9 - - + +
22B GLN* 2.9 48.6 + - + +
103C ILE* 5.0 10.1 - - + -
190C GLU* 3.4 28.9 - - - +
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Residues in contact with LEU 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 ASN* 3.2 21.6 + - + +
16B THR* 3.0 6.1 + - - +
18B VAL* 1.3 75.0 - - + +
20B LEU* 1.3 65.4 + - - +
21B HIS 2.8 4.0 - - - -
22B GLN* 2.7 26.7 + - - +
23B MET* 2.8 16.5 + - - +
83B LEU* 3.4 41.3 - - + +
86B GLN* 3.4 23.6 - - + +
87B LEU* 3.3 42.6 - - + +
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Residues in contact with LEU 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 THR* 2.8 27.8 + - + +
17B LEU* 3.7 3.8 - - + +
19B LEU* 1.3 71.2 - - - +
21B HIS* 1.3 58.9 + - - +
23B MET* 3.7 15.6 + - - -
66B ILE* 5.0 3.6 - - + -
70B PHE* 4.2 25.1 - - + -
87B LEU* 3.9 20.9 - - + -
147B ARG* 2.9 40.2 + - + -
150B ILE* 3.5 28.5 - - + -
151B MET* 3.6 23.1 - - + +
154B LEU* 3.9 19.5 - - + -
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Residues in contact with HIS 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 2.9 13.9 + - - +
18B VAL* 3.3 12.1 - - + +
19B LEU 2.7 4.6 + - - -
20B LEU* 1.3 72.3 - - - +
22B GLN* 1.3 63.9 + - + +
23B MET 2.8 11.3 + - - -
24B ARG* 2.9 35.6 + - + +
147B ARG* 5.4 0.2 + - - -
151B MET* 3.6 12.7 - - + +
98C ASN* 5.8 2.0 - - - -
100C TRP* 4.0 16.6 - + - -
103C ILE* 3.4 39.8 - - + +
104C ASP* 4.0 20.7 + - - -
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Residues in contact with GLN 22 (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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18B VAL* 2.9 34.0 + - + +
19B LEU* 2.7 23.9 + - - +
21B HIS* 1.3 76.5 - - + +
23B MET* 1.3 58.5 + - - +
24B ARG* 3.1 7.2 + - - +
80B GLN* 5.6 1.9 + - - -
83B LEU* 4.2 25.4 - - + +
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Residues in contact with MET 23 (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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19B LEU 2.8 16.7 + - - +
20B LEU* 4.0 29.4 - - + +
21B HIS 2.8 1.4 + - - -
22B GLN* 1.3 76.8 - - - +
24B ARG* 1.3 65.5 + - - +
25B ARG* 3.3 6.8 + - - +
70B PHE* 4.2 8.7 - - + -
79B TRP* 3.3 65.5 - - + -
80B GLN* 6.2 0.9 - - - +
83B LEU* 3.6 37.2 - - + +
84B LEU* 3.8 14.8 - - + -
87B LEU* 4.7 8.1 - - - -
147B ARG* 4.2 6.1 - - - -
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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