Contacts of the helix formed by residues 29 - 41 (chain C) in PDB entry 4XYN
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 LYS 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* 3.2 43.9 + - + +
23C GLY* 3.6 24.9 - - - +
28C LEU* 1.3 75.1 - - - +
30C LYS* 1.3 69.5 + - - +
31C SER* 3.0 8.1 - - - +
32C GLU* 2.8 41.1 + - + +
33C LEU* 2.9 10.7 + - - +
58C MET* 3.7 2.5 - - - -
67C GLY 5.1 0.9 - - - +
68C GLU* 3.3 25.8 + - + +
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Residues in contact with LYS 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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29C LYS* 1.3 73.7 - - - +
31C SER* 1.3 55.7 + - - +
33C LEU* 3.7 3.9 - - - +
34C LYS* 3.0 29.6 + - - +
51C GLN* 4.5 2.9 - - - +
54C VAL* 3.5 24.7 - - + +
55C ASP* 2.7 39.4 + - - +
58C MET* 3.3 42.9 - - + +
67C GLY* 4.9 7.1 + - - +
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Residues in contact with SER 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* 2.5 37.5 + - - -
29C LYS* 3.0 7.7 - - - +
30C LYS* 1.3 78.7 - - - +
32C GLU* 1.3 63.1 + - - +
34C LYS* 3.5 8.5 + - - +
35C GLU* 3.1 32.7 + - - +
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Residues in contact with GLU 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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18C TYR* 3.1 30.4 - - - +
19C SER 3.2 1.2 - - - +
21C ARG* 4.2 5.4 - - + -
22C GLU* 2.6 43.1 + - - +
27C LYS 3.3 0.2 - - - +
28C LEU* 3.3 14.3 - - + -
29C LYS* 2.8 38.1 + - + +
31C SER* 1.3 72.9 - - - +
33C LEU* 1.3 53.9 + - - +
35C GLU* 3.1 12.0 + - - +
36C LEU* 2.8 33.8 + - - +
501C CA 2.5 27.1 - - - -
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Residues in contact with LEU 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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28C LEU* 4.5 23.6 - - + +
29C LYS 2.9 14.5 + - - +
30C LYS* 3.7 5.2 - - - +
32C GLU* 1.3 75.3 - - - +
34C LYS* 1.3 60.5 + - - +
36C LEU* 3.6 9.4 - - + +
37C ILE* 2.9 55.2 + - + +
48C ILE* 6.1 0.2 - - + -
54C VAL* 5.4 3.1 - - + +
57C VAL* 4.0 14.1 - - + -
58C MET* 4.0 30.5 - - + +
61C LEU* 4.0 30.3 - - + -
69C CYS* 4.9 2.5 - - + -
74C PHE* 5.5 0.7 - - + -
77C PHE* 4.4 9.2 - - + -
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Residues in contact with LYS 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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30C LYS 3.0 18.5 + - - +
31C SER* 3.7 8.1 - - - +
32C GLU 3.3 0.2 - - - -
33C LEU* 1.3 73.0 - - - +
35C GLU* 1.3 62.1 + - + +
37C ILE* 4.7 3.8 - - - -
38C ASN* 2.8 48.1 + - - +
48C ILE* 3.2 43.1 - - + +
49C LYS* 4.2 15.4 + - - +
54C VAL* 4.0 19.0 - - + +
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Residues in contact with GLU 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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18C TYR* 3.6 6.5 - - + -
21C ARG* 2.5 50.9 + - - +
22C GLU* 3.7 17.1 - - - +
31C SER* 3.1 18.7 + - - +
32C GLU* 3.1 13.6 + - - +
34C LYS* 1.3 76.2 - - + +
36C LEU* 1.3 57.3 + - - +
38C ASN* 4.8 1.8 - - - -
39C ASN* 2.8 40.9 + - - +
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Residues in contact with LEU 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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14C VAL* 3.8 26.0 - - + +
15C PHE* 4.5 1.3 - - - -
18C TYR* 3.6 30.0 - - + -
28C LEU* 4.4 11.7 - - + -
32C GLU 2.8 15.0 + - - +
33C LEU* 3.6 9.2 - - + +
34C LYS 3.1 0.2 - - - -
35C GLU* 1.3 73.0 - - - +
37C ILE* 1.3 66.0 + - + +
40C GLU* 2.7 39.8 + - + +
41C LEU* 3.7 7.6 + - + -
74C PHE* 4.0 27.1 - - + -
77C PHE* 5.2 2.2 - - + -
4D LEU* 3.9 26.0 - - + -
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Residues in contact with ILE 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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33C LEU* 2.9 40.3 + - + +
34C LYS 4.0 2.2 - - - +
36C LEU* 1.3 72.7 - - + +
38C ASN* 1.3 68.1 + - - +
41C LEU* 3.1 28.7 + - + +
42C SER* 3.6 3.6 + - - -
45C LEU* 3.7 27.3 - - + +
46C GLU 4.5 1.8 - - - +
47C GLU* 5.6 0.2 - - - -
48C ILE* 3.5 41.7 - - + -
57C VAL* 4.5 8.3 - - + -
77C PHE* 3.6 37.2 - - + -
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Residues in contact with ASN 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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34C LYS* 2.8 35.6 + - - +
35C GLU* 4.2 2.9 - - - +
37C ILE* 1.3 80.5 - - - +
39C ASN* 1.3 65.5 + - - +
42C SER* 3.7 18.4 - - - +
47C GLU* 3.3 27.3 + - + +
48C ILE* 2.6 54.1 + - - +
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Residues in contact with ASN 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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18C TYR* 3.1 30.7 + - - +
21C ARG* 4.2 10.5 - - - +
35C GLU* 2.8 23.5 + - - +
38C ASN* 1.3 86.7 - - - +
40C GLU* 1.3 65.8 + - - +
41C LEU 3.7 0.2 - - - -
42C SER* 4.8 5.3 + - - -
2D SER* 4.8 2.1 - - - -
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Residues in contact with GLU 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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14C VAL* 3.6 21.6 - - + +
17C GLN* 3.3 18.1 + - - -
18C TYR* 2.5 44.6 + - + +
36C LEU* 2.7 19.0 + - + +
39C ASN* 1.3 82.9 - - - +
41C LEU* 1.3 63.7 + - - +
42C SER 3.7 1.8 - - - -
2D SER* 2.5 45.5 + - - +
4D LEU* 4.0 11.8 - - + +
5D GLU* 3.4 8.1 - - - +
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Residues in contact with LEU 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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36C LEU* 3.7 2.9 + - + -
37C ILE* 3.1 20.7 + - + +
40C GLU* 1.3 84.8 - - - +
42C SER* 1.3 53.8 + - - +
43C HIS 3.0 3.6 - - - -
44C PHE* 2.7 31.9 + - + -
45C LEU* 2.8 44.5 + - + -
77C PHE* 3.9 23.1 - - + -
81C VAL* 4.5 5.4 - - + -
4D LEU* 3.9 17.9 - - + -
5D GLU* 3.1 14.4 - - + -
8D MET* 3.6 38.4 - - + -
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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