Contacts of the helix formed by residues 13 - 22 (chain B) in PDB entry 1NS3
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 LEU 13 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A LEU* 3.3 38.8 - - + -
14A LEU* 5.4 7.0 - - + +
17A ILE* 4.1 18.6 - - + -
12B GLY* 1.3 68.9 - - - -
14B LEU* 1.3 65.6 + - - +
16B CYS* 3.1 5.3 + - + -
17B ILE* 2.7 46.3 + - + +
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Residues in contact with LEU 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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12B GLY 3.5 0.2 - - - -
13B LEU* 1.3 76.6 - - - +
15B GLY* 1.3 68.2 + - - +
17B ILE* 3.3 17.3 - - + +
18B ILE* 2.9 60.1 + - + +
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Residues in contact with GLY 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 ARG* 3.6 27.6 - - - -
12B GLY* 3.4 4.6 + - - +
13B LEU 3.3 1.0 - - - -
14B LEU* 1.3 80.5 - - - +
16B CYS* 1.3 63.4 + - - +
18B ILE* 5.2 1.3 - - - -
19B THR* 2.8 25.5 + - - -
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Residues in contact with CYS 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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13A LEU* 5.2 14.1 - - - -
11B ARG* 3.8 3.2 - - - +
12B GLY 2.8 20.4 + - - +
13B LEU* 3.9 3.8 - - + +
15B GLY* 1.3 68.9 - - - +
17B ILE* 1.3 68.1 + - - +
20B SER* 2.7 44.8 + - - -
37B SER* 4.7 18.6 - - - +
38B THR 4.7 13.7 - - - -
39B ALA* 5.5 0.9 - - - -
224D VAL* 4.2 13.7 - - + -
226D VAL* 4.5 18.8 - - + -
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Residues in contact with ILE 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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13A LEU* 4.2 11.0 - - + +
14A LEU* 4.0 45.3 - - + +
13B LEU* 2.7 52.6 + - + +
14B LEU* 3.3 32.5 - - + +
16B CYS* 1.3 77.0 - - - +
18B ILE* 1.3 60.9 + - + +
20B SER* 3.5 4.3 + - - -
21B LEU* 3.3 21.1 + - - +
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Residues in contact with ILE 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 LEU* 2.9 52.7 + - + +
15B GLY* 4.2 1.3 - - - +
17B ILE* 1.3 70.8 - - + +
19B THR* 1.3 68.3 + - - +
21B LEU* 2.9 21.0 + - + +
22B THR* 3.0 30.5 + - + +
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Residues in contact with THR 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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11B ARG* 3.6 16.5 + - - -
15B GLY* 2.8 28.4 + - - -
16B CYS 3.8 2.0 - - - -
18B ILE* 1.3 75.5 - - - +
20B SER* 1.3 56.7 + - - +
22B THR* 3.5 7.1 + - - -
23B GLY* 2.8 26.2 + - - -
24B ARG 4.2 4.3 + - - +
25B ASP* 3.8 21.4 - - + -
65B ALA* 3.5 24.5 - - + +
224D VAL* 3.7 19.7 - - + -
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Residues in contact with SER 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 CYS* 2.7 31.5 + - - -
17B ILE* 3.8 5.4 - - - -
19B THR* 1.3 72.0 - - - +
21B LEU* 1.3 62.4 + - - +
23B GLY 4.1 0.9 - - - -
37B SER 5.4 0.3 + - - -
38B THR* 5.6 2.3 - - - -
39B ALA 5.7 1.4 + - - -
220D LYS 4.4 0.5 - - - +
221D GLY* 3.4 12.5 - - - -
222D SER* 2.7 50.3 + - - +
224D VAL* 3.6 15.0 - - - -
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Residues in contact with LEU 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 ILE 3.3 12.5 + - - +
18B ILE* 2.9 15.6 + - + +
20B SER* 1.3 78.8 - - - +
22B THR* 1.3 69.9 + - + +
23B GLY* 3.5 0.5 + - - -
220D LYS 5.3 3.1 - - - +
221D GLY* 5.6 0.7 - - - -
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Residues in contact with THR 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 ILE* 3.0 30.9 + - + +
19B THR* 3.5 4.5 + - - -
21B LEU* 1.3 81.6 - - + +
23B GLY* 1.3 63.3 + - - +
24B ARG* 3.0 35.5 + - + +
70B PRO* 4.5 5.9 - - - +
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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