Contacts of the helix formed by residues 29 - 42 (chain G) in PDB entry 1N13
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 THR 29 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27G GLY 3.9 0.3 - - - -
28G GLU* 1.3 85.4 - - + +
30G PRO* 1.3 76.6 - - - +
31G LEU 3.6 2.4 + - - -
32G ASN* 2.6 39.0 + - - +
33G ALA* 2.9 23.2 + - - +
153H LEU* 3.8 7.3 - - - +
122J THR* 5.7 4.3 - - + -
126J MET* 3.8 24.4 - - + +
129J ILE* 5.2 3.1 - - + -
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Residues in contact with PRO 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29G THR* 1.3 86.0 - - - +
31G LEU* 1.3 57.3 + - - +
33G ALA* 3.2 3.6 + - - +
34G PHE* 2.9 28.1 + - - +
81H ILE* 3.5 27.5 - - + +
153H LEU* 4.0 24.7 - - + -
7003H MRD 4.5 7.0 - - + +
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Residues in contact with LEU 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29G THR* 3.3 1.2 + - - -
30G PRO* 1.3 79.8 - - - +
32G ASN* 1.3 57.0 + - - +
34G PHE* 3.4 5.8 + - + +
35G ASP* 2.9 28.8 + - - +
7003H MRD 3.6 38.1 - - + +
108J MET* 3.7 25.3 - - - +
109J GLU* 3.4 37.0 - - + +
126J MET* 3.6 15.7 - - + -
7013J AG2 3.7 33.9 - - + +
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Residues in contact with ASN 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27G GLY* 4.4 2.0 - - - -
28G GLU 4.3 5.4 - - - +
29G THR* 2.6 46.4 + - - +
31G LEU* 1.3 73.3 - - - +
33G ALA* 1.3 62.0 + - - +
35G ASP* 3.6 5.8 - - - +
36G GLY 2.9 22.3 + - - -
108J MET* 3.8 10.1 - - - +
126J MET* 3.0 41.5 - - - +
129J ILE* 3.6 30.4 - - + +
130J GLY* 3.8 4.9 + - - -
133J MET* 3.5 14.2 - - - +
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Residues in contact with ALA 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G SER* 3.9 8.2 - - - +
26G GLU 3.8 4.3 - - - -
27G GLY* 3.8 18.3 - - - +
29G THR 2.9 13.2 + - - +
30G PRO* 3.5 9.0 - - + +
32G ASN* 1.3 76.2 - - - +
34G PHE* 1.3 59.6 + - - +
36G GLY* 3.3 1.4 + - - -
37G ALA* 2.9 28.4 + - - +
81H ILE* 5.0 0.4 - - + -
153H LEU* 3.8 19.3 - - + -
155H CYS* 3.7 20.4 - - + +
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Residues in contact with PHE 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G PRO 2.9 16.5 + - - +
31G LEU* 3.6 5.2 - - + +
33G ALA* 1.3 73.8 - - - +
35G ASP* 1.3 63.1 + - - +
37G ALA* 3.0 4.7 + - - +
38G LEU* 3.0 46.5 + - + +
48G LEU* 5.0 0.7 - - + -
77H TYR* 4.0 15.3 - + - -
79H TYR* 3.8 41.3 - + - -
81H ILE* 4.5 0.7 - - + -
155H CYS* 3.8 15.9 - - - +
157H PHE* 3.9 15.7 - + - -
7003H MRD 3.6 40.4 - - + -
52I SER 3.4 23.1 - - - -
7013J AG2 3.8 17.3 - - + -
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Residues in contact with ASP 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31G LEU 2.9 17.0 + - - +
32G ASN* 3.6 6.3 - - - +
34G PHE* 1.3 75.7 - - - +
36G GLY* 1.3 63.7 + - - +
38G LEU* 3.2 3.8 + - - +
39G LEU* 3.0 25.8 + - - +
106J LEU* 3.9 2.8 - - - +
108J MET* 3.8 21.5 - - + +
130J GLY* 4.0 5.9 - - - -
133J MET* 5.1 2.5 - - - +
134J ARG* 2.7 36.1 + - - -
7013J AG2 2.9 41.2 + - - -
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Residues in contact with GLY 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G SER* 3.3 23.0 - - - -
32G ASN 2.9 15.5 + - - -
33G ALA 3.3 1.3 + - - -
34G PHE 3.2 0.2 - - - -
35G ASP* 1.3 77.6 - - - +
37G ALA* 1.3 55.0 + - - +
39G LEU* 3.3 10.8 + - - +
40G ASN* 2.9 28.8 + - - +
133J MET* 3.7 12.1 - - - +
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Residues in contact with ALA 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G GLY* 3.7 7.6 - - - +
24G SER* 3.9 6.1 - - - -
25G SER* 3.4 6.2 - - - -
33G ALA 2.9 13.0 + - - +
34G PHE 3.0 8.7 + - - +
36G GLY* 1.3 73.1 - - - +
38G LEU* 1.3 61.2 + - - +
40G ASN* 3.3 3.5 + - - +
41G ALA* 2.9 28.3 + - - +
155H CYS* 3.7 33.0 - - - +
157H PHE* 3.8 16.6 - - + -
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Residues in contact with LEU 38 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34G PHE* 3.0 38.0 + - + +
35G ASP 3.6 5.4 - - - +
37G ALA* 1.3 75.4 - - - +
39G LEU* 1.3 58.2 + - - +
41G ALA* 3.0 7.7 + - - +
42G GLY 2.9 23.4 + - - -
43G ILE* 3.0 18.6 + - + +
44G GLY* 3.7 11.9 - - - -
48G LEU* 3.7 23.1 - - + -
157H PHE* 3.4 40.2 - - + -
52I SER 4.1 0.4 - - - +
7013J AG2 3.4 36.8 - - - +
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Residues in contact with LEU 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B ARG* 4.4 3.8 + - - -
142B GLU* 5.4 0.7 - - - +
35G ASP* 3.0 21.5 + - - +
36G GLY* 3.5 14.6 - - - +
38G LEU* 1.3 77.8 - - - +
40G ASN* 1.3 61.0 + - - +
42G GLY* 3.1 13.7 + - - -
44G GLY* 3.8 21.3 - - - +
45G ASN* 4.0 11.2 - - - +
133J MET* 4.6 17.0 - - + +
134J ARG* 3.7 51.4 - - + +
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Residues in contact with ASN 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B GLU* 4.3 28.8 + - - +
101B LYS* 5.9 0.7 + - - -
140B ARG* 3.2 20.6 + - - +
22G ALA 4.1 2.6 - - - +
23G GLY* 3.2 8.1 - - - -
24G SER* 2.9 43.0 + - - +
25G SER* 5.0 0.4 - - - -
36G GLY 2.9 13.7 + - - +
37G ALA 3.5 4.9 - - - +
38G LEU 3.2 0.2 - - - -
39G LEU* 1.3 75.8 - - - +
41G ALA* 1.3 57.5 + - - +
146H VAL* 5.4 1.0 - - - +
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Residues in contact with ALA 41 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B ASP* 5.0 0.2 - - - +
140B ARG* 3.2 16.2 + - - +
21G VAL* 3.5 25.3 - - + +
22G ALA* 3.3 35.8 - - - +
23G GLY 3.7 1.1 - - - +
37G ALA 2.9 16.9 + - - +
38G LEU 3.0 5.6 + - - +
40G ASN* 1.3 77.9 - - - +
42G GLY* 1.3 56.5 + - - +
43G ILE* 3.6 1.6 - - + -
157H PHE* 4.0 17.0 - - + -
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Residues in contact with GLY 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B ARG* 3.4 23.3 - - - -
142B GLU* 4.2 7.7 - - - +
38G LEU 2.9 2.8 + - - -
39G LEU 3.1 11.5 + - - -
40G ASN 3.4 0.4 + - - -
41G ALA* 1.3 79.5 - - - +
43G ILE* 1.3 62.7 + - - +
44G GLY 3.6 3.1 + - - -
64H LEU* 3.4 16.2 - - - +
67H LEU* 5.8 0.3 - - - +
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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