Contacts of the helix formed by residues 29 - 44 (chain C) in PDB entry 2NUP
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 ASP 29 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22C GLU* 3.1 22.2 - - - +
30C LEU* 1.3 68.2 + - - +
31C GLN* 3.0 33.0 + - + +
32C GLN* 3.2 6.1 + - - +
33C TYR* 3.8 25.5 + - - -
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Residues in contact with LEU 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499B ARG* 4.9 12.1 - - + -
4C LEU* 3.4 21.8 - - + -
20C MET* 3.2 48.7 - - + -
21C GLN 5.6 0.4 - - - +
22C GLU* 3.7 33.4 + - + +
29C ASP* 1.3 73.8 - - - +
31C GLN* 1.3 64.9 + - - +
33C TYR* 3.6 3.0 + - - +
34C GLN* 2.8 46.2 + - + +
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Residues in contact with GLN 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C GLU* 5.4 0.2 + - - -
29C ASP* 3.0 33.3 + - + +
30C LEU* 1.3 78.7 - - - +
32C GLN* 1.3 99.5 + - - +
34C GLN* 3.4 6.5 - - - +
35C SER* 3.3 15.6 + - - -
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Residues in contact with GLN 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ASP 3.2 5.0 + - - +
31C GLN* 1.3 97.1 + - - +
33C TYR* 1.3 83.4 + - + +
34C GLN 2.9 4.0 - - - -
35C SER* 2.5 37.7 + - - +
36C GLN* 3.2 18.8 + - + +
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Residues in contact with TYR 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C LEU* 4.5 5.6 - - + +
29C ASP 3.8 20.6 - - - +
30C LEU* 3.6 5.1 + - - +
32C GLN* 1.3 97.9 + - + +
34C GLN* 1.3 61.5 + - - +
36C GLN* 3.4 28.2 - - - +
37C ALA* 3.0 22.2 + - - +
56C ALA* 3.9 13.4 + - + -
58C ALA* 5.4 1.2 + - - +
59C MET* 3.1 41.1 - - + +
61C PHE* 3.8 11.2 - + + -
74C LEU* 3.3 33.2 - - + -
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Residues in contact with GLN 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498B LEU 3.4 26.4 + - - +
499B ARG* 4.0 8.2 - - - +
500B PRO* 4.8 1.2 - - - +
4C LEU* 5.0 3.8 - - + +
6C MET* 4.7 6.7 - - - -
20C MET* 3.4 41.4 - - + -
30C LEU* 2.8 38.2 + - + +
31C GLN* 3.4 7.5 - - - +
32C GLN 2.8 0.2 + - - -
33C TYR* 1.3 73.6 - - - +
35C SER* 1.3 66.6 + - - +
37C ALA* 3.2 7.7 + - - +
38C LYS* 3.0 53.5 + - - +
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Residues in contact with SER 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C GLN 3.3 7.4 + - - -
32C GLN* 2.5 24.7 + - - +
34C GLN* 1.3 78.2 - - - +
36C GLN* 1.3 59.0 + - - +
38C LYS* 2.9 12.8 + - - +
39C GLN* 2.7 47.2 + - - +
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Residues in contact with GLN 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C GLN* 3.2 24.2 + - + +
33C TYR* 3.4 35.7 - - - +
35C SER* 1.3 84.0 + - - +
37C ALA* 1.3 56.7 + - - +
39C GLN* 2.7 32.5 + - + +
40C LEU* 2.8 14.7 + - - +
56C ALA* 4.3 4.2 - - - +
61C PHE* 3.5 12.0 - - + -
153C ILE* 3.8 21.4 - - + +
154C GLU* 3.5 24.9 + - - -
157C LEU* 4.0 13.1 - - + +
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Residues in contact with ALA 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C LEU* 5.2 4.0 - - + -
6C MET* 3.8 22.2 - - - -
33C TYR 3.0 15.4 + - - +
34C GLN* 3.3 10.5 - - - +
36C GLN* 1.3 77.3 - - - +
38C LYS* 1.3 62.4 + - - +
40C LEU* 3.2 5.7 + - - +
41C PHE* 3.1 28.6 + - + -
61C PHE* 4.3 8.4 - - + -
72C LEU* 3.7 25.6 - - + +
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Residues in contact with LYS 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494B SER* 4.2 23.5 + - - +
495B GLU* 6.0 0.2 - - - +
497B MET* 4.3 13.9 + - - +
498B LEU 5.2 0.8 + - - -
499B ARG* 5.5 1.6 - - - +
6C MET* 4.3 22.9 - - + -
15C PRO* 5.6 6.7 - - + +
34C GLN* 3.0 39.1 + - - +
35C SER* 2.9 10.8 + - - +
37C ALA* 1.3 73.3 - - - +
39C GLN* 1.3 68.6 + - - +
41C PHE* 3.6 12.6 + - + +
42C ARG* 3.3 21.0 + - - +
110C TYR* 4.8 9.3 + - - -
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Residues in contact with GLN 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C SER* 2.7 31.5 + - - +
36C GLN* 2.7 19.3 + - + +
38C LYS* 1.3 80.5 + - - +
40C LEU* 1.3 61.4 + - - +
42C ARG* 3.3 21.2 + - - +
43C LYS* 3.1 33.9 + - - +
157C LEU* 3.2 23.8 - - + -
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Residues in contact with LEU 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C GLN 2.8 10.2 + - - +
37C ALA* 3.4 10.8 - - - +
39C GLN* 1.3 75.4 - - - +
41C PHE* 1.3 68.2 + - + +
43C LYS* 2.9 6.2 + - + +
44C LEU* 2.8 51.6 + - + +
54C LEU* 3.4 33.4 - - + -
61C PHE* 5.2 3.1 - - + -
63C TYR* 3.9 20.6 - - + -
72C LEU* 4.4 20.4 - - + -
153C ILE* 5.7 2.5 - - + -
156C VAL* 4.3 23.8 - - + -
157C LEU* 3.9 8.7 - - + +
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Residues in contact with PHE 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C MET* 3.7 53.2 - - + -
8C ALA* 3.6 32.5 - - + -
9C ARG 6.5 0.2 - - - -
10C VAL* 3.9 11.9 - - - +
12C ASP 5.1 0.3 - - - -
13C GLY* 4.1 25.1 + - - +
15C PRO* 5.8 3.4 - - + -
37C ALA 3.1 14.0 + - - -
38C LYS* 3.8 15.3 - - + +
39C GLN 3.4 0.2 - - - -
40C LEU* 1.3 78.8 - - + +
42C ARG* 1.3 64.0 + - - +
44C LEU* 3.5 23.0 + - + +
70C CYS* 3.8 33.0 - - + -
72C LEU* 4.0 18.6 - - + -
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Residues in contact with ARG 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C VAL 5.3 0.3 - - - +
11C ALA 5.3 3.5 - - - +
12C ASP 5.1 8.7 - - - +
13C GLY* 5.0 0.4 - - - -
38C LYS 3.3 9.7 + - - +
39C GLN* 3.3 24.0 + - - +
40C LEU 3.1 0.4 - - - -
41C PHE* 1.3 82.9 - - - +
43C LYS* 1.3 77.9 + - + +
44C LEU 3.6 5.2 - - - +
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Residues in contact with LYS 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C GLN* 3.2 25.8 + - - +
40C LEU* 2.9 8.9 + - + +
42C ARG* 1.3 91.7 - - + +
44C LEU* 1.3 66.7 + - - +
45C ASN* 3.2 19.4 + - - +
48C SER* 4.0 1.7 + - - -
156C VAL* 4.2 26.7 - - + +
157C LEU* 3.0 39.6 + - + +
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Residues in contact with LEU 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C VAL* 3.4 29.5 - - + +
11C ALA 4.7 1.7 - - - +
40C LEU* 2.8 45.2 + - + +
41C PHE* 3.6 13.0 - - + +
42C ARG 3.3 8.0 - - - +
43C LYS* 1.3 74.9 - - + +
45C ASN* 1.3 59.5 + - - +
48C SER* 3.3 17.0 - - - -
49C PRO* 5.5 0.2 - - + -
63C TYR* 3.4 31.4 - - + +
65C ILE* 4.0 8.7 - - + -
70C CYS* 3.5 39.0 - - + -
156C VAL* 6.1 1.1 - - + -
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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