Contacts of the helix formed by residues 26 - 41 (chain C) in PDB entry 3N93
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 ASN 26 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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-321B GLN* 5.1 3.8 + - - -
-29B TYR* 5.2 6.8 + - - -
27C LEU* 1.3 93.9 + - - +
28C ARG* 4.3 3.9 - - + +
29C ALA* 4.0 21.3 - - - +
30C GLN* 3.3 27.8 + - - +
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Residues in contact with LEU 27 (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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70B GLY* 3.4 26.5 - - - +
71B VAL* 4.3 15.8 - - + +
102B LEU* 4.0 10.7 - - + +
26C ASN* 1.3 96.6 - - - +
28C ARG* 1.3 61.0 + - + +
30C GLN* 3.8 9.0 - - + +
31C ALA* 3.2 26.0 + - - +
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Residues in contact with ARG 28 (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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102B LEU* 4.0 22.3 - - + +
103B ASP* 3.0 29.9 + - - -
26C ASN* 3.3 4.4 - - + +
27C LEU* 1.3 77.0 - - + +
29C ALA* 1.3 59.9 + - - +
30C GLN 3.3 0.2 - - - -
31C ALA* 3.6 3.2 + - - +
32C ALA* 3.0 26.7 + - - +
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Residues in contact with ALA 29 (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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-321B GLN* 3.8 35.8 - - + +
26C ASN 3.9 17.9 + - - +
27C LEU 3.5 0.2 - - - -
28C ARG* 1.3 77.1 - - - +
30C GLN* 1.3 60.0 + - - +
32C ALA* 3.6 8.4 + - - +
33C ALA* 3.1 26.3 + - - +
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Residues in contact with GLN 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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69B ASN* 3.2 32.1 + - - +
70B GLY* 5.4 4.7 - - - -
71B VAL* 3.8 15.3 - - + -
26C ASN 3.3 19.5 + - - +
27C LEU* 3.8 10.8 - - + +
28C ARG 3.3 0.4 - - - -
29C ALA* 1.3 76.7 - - - +
31C ALA* 1.3 65.9 + - - +
33C ALA* 3.1 8.8 + - - +
34C ASN* 3.1 32.6 + - - +
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Residues in contact with ALA 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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71B VAL* 3.6 12.7 - - + +
73B TYR* 4.2 3.9 + - - -
100B PRO* 3.9 34.3 - - + +
102B LEU* 4.6 5.2 - - + -
27C LEU 3.2 16.7 + - - +
28C ARG* 3.8 6.5 - - - +
30C GLN* 1.3 78.1 - - - +
32C ALA* 1.3 57.5 + - - +
34C ASN* 3.3 6.3 + - - +
35C ALA* 2.9 29.4 + - - +
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Residues in contact with ALA 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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-321B GLN* 6.0 7.2 - - + +
-318B ALA* 5.8 4.0 - - + -
28C ARG 3.0 18.5 + - - +
29C ALA* 3.8 9.6 - - - +
30C GLN 3.2 0.2 - - - -
31C ALA* 1.3 77.2 - - - +
33C ALA* 1.3 59.4 + - - +
35C ALA* 3.5 6.6 + - - +
36C HIS* 2.9 39.2 + - + +
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Residues in contact with ALA 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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-297B SER* 5.5 9.7 + - - +
69B ASN* 5.8 1.8 - - - +
29C ALA 3.1 14.5 + - - +
30C GLN* 3.1 16.1 + - - +
32C ALA* 1.3 76.0 - - - +
34C ASN* 1.3 66.2 + - - +
36C HIS* 3.5 7.2 + - - +
37C LEU* 3.2 19.9 + - - +
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Residues in contact with ASN 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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68B PHE* 3.2 38.7 + - + -
69B ASN* 3.3 26.2 + - - -
71B VAL* 3.4 19.4 - - - +
73B TYR* 2.8 30.3 + - - +
30C GLN* 3.1 12.3 + - - +
31C ALA 3.6 2.5 - - - +
33C ALA* 1.3 76.0 - - - +
35C ALA* 1.3 53.9 + - - +
36C HIS 3.1 0.2 - - - -
37C LEU* 3.1 8.4 + - - +
38C MET* 2.6 41.6 + - + +
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Residues in contact with ALA 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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73B TYR* 4.8 1.1 + - + -
100B PRO* 6.3 3.6 - - + -
31C ALA 2.9 16.8 + - - +
32C ALA* 3.7 9.9 - - - +
33C ALA 3.4 0.2 - - - -
34C ASN* 1.3 75.7 - - - +
36C HIS* 1.3 61.4 + - + +
38C MET* 3.5 12.1 + - - +
39C ALA* 2.9 28.2 + - - +
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Residues in contact with HIS 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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-318B ALA* 3.1 51.6 + - + +
-317B THR* 4.5 4.4 + - - +
-297B SER* 5.1 12.5 + - - +
-295B LEU* 5.7 2.5 - - + +
32C ALA* 2.9 30.5 + - + +
33C ALA* 3.9 6.3 - - - +
34C ASN 3.1 0.8 - - - -
35C ALA* 1.3 79.7 - - + +
37C LEU* 1.3 63.8 + - - +
39C ALA* 3.4 7.9 + - - +
40C GLN* 3.2 39.8 + - - +
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Residues in contact with LEU 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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46B GLN* 5.9 6.5 - - + -
47B ILE* 4.6 8.5 - - + -
68B PHE* 4.1 23.6 - - + -
69B ASN* 5.5 5.4 - - - +
33C ALA 3.2 13.0 + - - +
34C ASN* 3.1 9.3 + - - +
36C HIS* 1.3 76.6 - - - +
38C MET* 1.3 56.9 + - - +
40C GLN* 3.2 17.2 + - - +
41C ILE* 2.9 49.5 + - + +
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Residues in contact with MET 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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47B ILE* 4.0 36.8 - - + -
65B PRO* 4.2 10.3 - - + -
68B PHE* 4.2 7.4 - - + -
73B TYR* 3.8 40.6 - - + +
93B ILE 4.2 0.3 - - - +
95B TYR* 3.7 33.9 + - + +
98B CYS* 4.2 24.7 - - + +
34C ASN* 2.6 24.9 + - + +
35C ALA* 3.6 9.9 - - - +
37C LEU* 1.3 73.6 - - - +
39C ALA* 1.3 56.1 + - - +
41C ILE* 4.6 3.8 - - - -
42C NH2 2.8 26.2 + - - -
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Residues in contact with ALA 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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92B LYS* 3.1 29.6 + - - -
35C ALA 2.9 18.7 + - - +
36C HIS* 3.7 11.7 - - - +
37C LEU 3.2 0.4 - - - -
38C MET* 1.3 76.2 - - - +
40C GLN* 1.3 61.3 + - + +
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Residues in contact with GLN 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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-298B GLN 4.1 11.2 + - - +
-297B SER* 3.3 31.4 + - - +
-296B GLY* 4.4 3.2 - - - +
92B LYS* 4.1 13.3 - - - +
36C HIS* 3.2 23.9 + - - +
37C LEU* 3.2 20.2 + - - +
39C ALA* 1.3 76.3 - - + +
41C ILE* 1.3 68.9 + - + +
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Residues in contact with ILE 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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45B ASP* 5.2 1.1 - - - +
46B GLN* 3.8 36.3 - - + +
47B ILE* 4.5 11.2 - - + -
91B SER 4.0 4.9 - - - +
92B LYS* 3.5 10.0 - - - +
93B ILE* 2.8 44.6 + - + +
95B TYR* 4.4 11.7 - - + -
37C LEU* 2.9 40.7 + - + +
38C MET* 4.1 3.1 - - - +
40C GLN* 1.3 83.2 - - + +
42C NH2 1.3 46.9 + - - +
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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