Contacts of the helix formed by residues 17 - 29 (chain A) in PDB entry 3NOR
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 17 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A VAL* 1.3 71.7 - - - +
18A GLN* 1.3 68.6 + - - +
19A LEU* 5.3 1.8 - - - +
20A ASP* 3.0 42.6 + - - +
49A SER* 3.8 16.3 + - - -
50A SER* 6.0 3.0 - - - -
73A GLY 2.8 12.2 + - - +
74A GLY* 3.5 17.7 - - - +
104A CYS* 5.6 1.8 - - - -
155A ILE* 3.8 24.3 - - + +
232A CIT 3.1 31.6 - - + +
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Residues in contact with GLN 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A VAL* 3.2 13.9 + - - -
17A GLN* 1.3 74.9 - - - +
19A LEU* 1.3 73.6 + - - +
21A LEU* 2.9 6.8 + - - +
22A THR* 2.8 58.6 + - - +
48A ALA* 3.7 24.4 - - + +
49A SER* 4.8 0.8 + - - -
50A SER* 4.3 13.8 + - - +
52A LEU* 4.2 24.9 - - + +
54A LEU* 4.1 16.8 - - + -
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Residues in contact with LEU 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A GLN* 3.0 3.2 + - + +
18A GLN* 1.3 87.8 + - - +
20A ASP* 1.3 66.3 + - - +
21A LEU 3.1 0.9 + - - -
22A THR* 3.4 15.0 - - - +
23A GLY* 3.1 31.9 + - - +
24A PRO* 4.1 0.5 - - - +
155A ILE* 3.8 38.3 - - + +
156A THR* 3.9 23.9 - - + -
159A ILE* 5.1 2.7 - - + -
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Residues in contact with ASP 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A GLN* 3.1 31.5 - - - +
19A LEU* 1.3 76.3 - - - +
21A LEU* 1.3 56.6 + - - +
24A PRO* 3.1 22.5 - - - +
70A CYS* 5.2 0.3 - - - -
72A PRO* 3.5 16.3 - - + +
73A GLY* 2.8 28.4 + - - -
103A VAL* 3.7 27.1 - - + +
104A CYS* 3.2 17.1 - - - +
155A ILE* 3.4 26.7 + - - +
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Residues in contact with LEU 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PHE* 3.8 28.3 - - + -
11A LEU 3.7 22.9 - - - +
12A LEU* 4.1 20.9 - - + -
16A VAL* 4.6 4.3 - - + -
18A GLN* 2.9 8.1 + - - +
20A ASP* 1.3 78.8 - - - +
22A THR* 1.3 77.6 + - + +
23A GLY 3.3 2.0 - - - -
24A PRO* 3.3 6.6 - - - +
25A HIS* 2.9 36.2 + - + +
38A LEU* 3.7 26.9 - - + -
54A LEU* 4.6 8.1 - - + -
72A PRO* 4.2 15.0 - - + -
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Residues in contact with THR 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A GLN* 2.8 40.2 + - - +
19A LEU* 3.4 12.6 - - - +
21A LEU* 1.3 89.1 - - + +
23A GLY* 1.3 68.5 + - - +
25A HIS* 3.6 4.8 - - + +
26A ASP* 3.1 22.3 + - - +
54A LEU* 4.3 21.8 - - + -
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Residues in contact with GLY 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 3.1 19.5 + - - +
22A THR* 1.3 81.4 + - - +
24A PRO* 1.3 68.3 - - - +
26A ASP* 3.2 9.6 + - - +
27A VAL* 3.4 14.9 + - - +
159A ILE* 3.6 26.5 - - - +
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Residues in contact with PRO 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A PHE* 3.7 21.1 - - + -
19A LEU 4.1 1.3 - - - +
20A ASP 3.1 28.3 - - - +
21A LEU 3.3 8.7 - - - +
23A GLY* 1.3 85.5 - - - +
25A HIS* 1.3 59.7 + - - +
27A VAL* 3.3 0.8 + - + -
28A LEU* 2.9 32.2 + - + +
70A CYS* 4.8 6.7 - - - -
103A VAL* 4.9 0.2 - - + -
155A ILE 5.6 1.1 - - - +
156A THR 6.0 0.2 - - - -
158A GLY* 3.5 40.4 - - - +
159A ILE* 3.9 4.0 - - + +
161A PHE* 5.3 2.7 - - + -
162A ALA* 4.2 9.2 - - + -
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Residues in contact with HIS 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A PHE* 3.5 16.3 - + + -
21A LEU* 2.9 23.2 + - + +
22A THR* 3.6 11.0 - - + +
23A GLY 3.1 0.2 - - - -
24A PRO* 1.3 76.3 - - - +
26A ASP* 1.3 63.9 + - - +
28A LEU* 4.3 0.4 - - - +
29A ALA* 2.8 49.4 + - + +
36A VAL* 3.4 33.9 + - + +
38A LEU* 3.9 32.1 - - + +
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Residues in contact with ASP 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A THR 3.1 14.5 + - - +
23A GLY* 3.2 3.6 + - - +
25A HIS* 1.3 85.5 + - - +
27A VAL* 1.3 62.3 + - + +
29A ALA* 3.8 5.2 + - - +
30A SER* 2.9 25.1 + - - -
182A LEU* 4.2 12.9 - - + +
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Residues in contact with VAL 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLY 3.4 11.8 + - - +
24A PRO 3.3 6.0 + - - +
25A HIS 3.2 0.4 - - - -
26A ASP* 1.3 78.0 - - + +
28A LEU* 1.3 65.8 + - + +
30A SER* 3.1 20.6 + - - -
31A LEU* 4.0 4.2 + - + +
159A ILE* 3.9 28.5 - - + +
162A ALA* 3.6 25.6 - - + +
163A LEU* 3.9 25.8 - - + +
166A ALA* 5.5 3.1 - - + -
178A VAL* 4.1 10.0 - - + +
182A LEU* 4.0 19.5 - - + -
184A TYR* 6.1 2.5 - - + -
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Residues in contact with LEU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 3.6 42.2 - - + -
10A PHE* 4.1 11.9 - - + -
24A PRO* 2.9 26.0 + - + +
25A HIS* 4.3 2.0 - - - +
27A VAL* 1.3 75.0 - - + +
29A ALA* 1.3 56.3 + - - +
30A SER 3.0 0.2 - - - -
31A LEU* 3.0 43.6 + - + +
34A VAL* 3.3 14.5 - - - +
36A VAL* 4.6 2.5 - - + -
68A VAL* 4.7 3.6 - - + -
70A CYS* 6.2 0.4 - - + -
161A PHE* 6.2 1.6 - - + -
162A ALA* 3.8 34.3 - - + +
165A LEU* 4.5 22.2 - - + -
169A LEU* 5.4 1.1 - - + -
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Residues in contact with ALA 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A HIS* 2.8 34.5 + - + +
26A ASP* 4.2 7.9 - - - +
27A VAL 3.3 0.2 - - - -
28A LEU* 1.3 75.9 - - - +
30A SER* 1.3 59.6 + - - +
31A LEU 3.3 5.0 + - - +
34A VAL* 4.0 5.6 - - - +
36A VAL* 3.9 22.6 - - + +
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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