Contacts of the helix formed by residues 24 - 36 (chain A) in PDB entry 1N1E
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 GLY 24 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A GLY 3.3 3.8 - - - -
23A SER* 1.3 77.2 - - - +
25A ALA* 1.3 64.7 + - - -
26A PHE 3.3 2.7 - - - -
27A GLY 4.0 0.6 - - - +
28A THR* 2.9 26.9 + - - -
63A PHE* 3.8 10.1 - - - -
92A VAL 5.4 1.2 + - - -
400A NDE 3.3 37.6 + - - -
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Residues in contact with ALA 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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24A GLY* 1.3 71.0 - - - +
26A PHE* 1.3 58.0 + - - +
28A THR* 3.8 2.1 - - - -
29A ALA* 3.0 28.1 + - - +
63A PHE* 3.5 23.2 - - - +
64A LEU* 3.9 12.9 - - + +
157A ALA* 3.7 19.5 - - + +
274A ARG* 4.7 3.6 - - - +
400A NDE 2.8 29.2 + - - +
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Residues in contact with PHE 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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25A ALA* 1.3 76.4 - - - +
27A GLY* 1.3 62.1 + - - +
29A ALA* 3.2 2.5 + - + +
30A LEU* 2.8 66.4 + - + +
92A VAL* 3.8 16.4 - - + -
123A CYS* 4.1 11.2 - - + -
125A LYS* 5.7 0.4 - - - -
151A LEU* 4.0 13.9 - - + -
155A SER* 3.3 39.7 - - - -
157A ALA* 4.1 9.9 - - - -
160A VAL* 4.4 7.9 - - + -
192A PHE* 5.8 0.2 - + - -
400A NDE 3.0 66.7 + + + +
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Residues in contact with GLY 27 (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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20A VAL* 3.6 17.2 - - - +
22A GLY 3.2 25.1 - - - -
24A GLY 3.5 3.4 + - - +
25A ALA 3.5 0.4 - - - -
26A PHE* 1.3 77.5 - - - +
28A THR* 1.3 57.4 + - - +
30A LEU* 3.4 1.5 + - - -
31A ALA* 2.9 27.9 + - - +
43A VAL* 5.3 0.9 - - - -
92A VAL* 3.6 17.5 - - - +
400A NDE 4.0 2.4 + - - -
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Residues in contact with THR 28 (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 GLY 4.1 0.4 + - - -
23A SER* 3.4 4.2 + - - -
24A GLY 2.9 18.0 + - - -
25A ALA 3.8 3.4 - - - -
27A GLY* 1.3 74.5 - - - +
29A ALA* 1.3 65.5 + - - +
31A ALA* 3.2 8.3 + - + +
32A MET* 3.0 22.8 + - + +
43A VAL* 5.3 1.1 - - - -
60A ASN* 2.8 31.6 + - + -
64A LEU* 3.8 21.1 - - + -
69A LEU* 3.6 29.8 - - + -
73A ILE* 5.1 0.2 - - - +
75A PHE* 3.7 13.2 - - + -
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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 ALA 3.0 17.9 + - - +
26A PHE* 3.2 7.2 + - + +
28A THR* 1.3 76.3 - - - +
30A LEU* 1.3 61.3 + - - +
32A MET* 3.1 14.6 + - - +
33A VAL* 3.1 15.1 + - - +
64A LEU* 4.4 0.8 - - - +
157A ALA* 3.4 31.6 - - - +
160A VAL* 3.7 13.4 - - + +
161A ALA* 3.7 20.3 - - + +
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Residues in contact with LEU 30 (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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26A PHE* 2.8 57.3 + - + +
27A GLY* 3.9 4.7 - - - +
29A ALA* 1.3 69.6 - - - +
31A ALA* 1.3 61.2 + - - +
33A VAL* 3.3 5.5 + - + +
34A LEU* 2.9 33.6 + - - +
90A LEU* 3.9 18.8 - - + -
92A VAL* 4.4 5.2 - - + -
123A CYS* 3.5 32.1 - - + -
151A LEU* 4.6 4.5 - - + -
160A VAL* 4.3 6.7 - - + -
185A MET* 4.5 11.2 - - + +
192A PHE* 4.0 27.4 - - + -
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Residues in contact with ALA 31 (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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20A VAL* 4.3 5.7 - - + +
27A GLY 2.9 14.9 + - - +
28A THR* 3.2 11.4 + - + +
30A LEU* 1.3 75.9 - - - +
32A MET* 1.3 55.9 + - - +
34A LEU* 3.6 1.7 - - - +
35A SER* 2.8 30.7 + - - -
41A VAL* 3.9 17.9 - - + +
43A VAL* 3.6 28.7 - - + -
73A ILE* 3.5 14.0 - - + +
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Residues in contact with MET 32 (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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28A THR* 3.0 19.4 + - + +
29A ALA 3.1 9.4 + - - +
31A ALA* 1.3 74.1 - - - +
33A VAL* 1.3 62.5 + - - +
35A SER* 2.8 21.2 + - - +
36A LYS* 3.8 12.2 + - - +
67A VAL* 4.1 10.5 - - + -
68A GLN 3.5 17.9 - - - +
69A LEU* 4.0 12.6 - - + -
70A ALA* 3.6 29.6 - - + +
73A ILE* 3.6 10.3 - - + -
160A VAL 5.0 0.7 - - - +
161A ALA* 3.5 37.0 - - + +
162A THR* 5.6 0.4 - - - -
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Residues in contact with VAL 33 (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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29A ALA 3.1 4.8 + - - +
30A LEU* 3.5 9.9 - - + +
32A MET* 1.3 76.9 - - - +
34A LEU* 1.3 64.3 + - + +
36A LYS* 3.1 27.0 + - - +
37A LYS* 3.8 5.9 + - + +
160A VAL* 3.5 37.7 + - + +
185A MET* 3.4 35.7 - - + +
187A THR* 4.0 10.7 - - + +
192A PHE* 3.8 27.8 - - + -
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Residues in contact with LEU 34 (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 ALA* 3.9 19.3 - - + -
20A VAL* 4.0 13.9 - - + -
30A LEU 2.9 18.8 + - - +
31A ALA* 3.3 4.2 + - - +
33A VAL* 1.3 76.6 - - - +
35A SER* 1.3 56.7 + - - +
37A LYS* 2.9 6.1 + - + +
38A CYS* 2.9 49.8 + - - +
41A VAL* 3.7 12.8 - - + -
88A ILE* 4.5 6.7 - - + -
90A LEU* 3.9 30.7 - - + -
184A ILE* 4.7 11.4 - - + +
185A MET* 3.6 29.8 - - + -
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Residues in contact with SER 35 (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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31A ALA 2.8 19.5 + - - -
32A MET* 2.8 21.7 + - - +
33A VAL 3.2 0.2 - - - -
34A LEU* 1.3 72.0 - - - +
36A LYS* 1.3 61.8 + - - +
38A CYS 3.5 3.7 - - - +
41A VAL* 3.6 4.9 - - - +
70A ALA* 3.5 19.8 - - - +
72A ASN* 3.1 45.2 + - - +
73A ILE* 3.8 8.7 - - - -
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Residues in contact with LYS 36 (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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14A TYR* 3.7 14.7 - - - -
32A MET 3.9 11.9 - - - +
33A VAL* 3.1 13.1 + - - +
35A SER* 1.3 79.2 + - - +
37A LYS* 1.3 61.4 + - + +
38A CYS 3.7 0.2 - - - -
163A GLY* 4.3 13.9 - - - -
187A THR* 4.0 23.6 - - + -
189A ASP* 2.9 28.2 + - - +
191A SER* 3.1 21.0 + - - -
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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