Contacts of the helix formed by residues 6 - 24 (chain C) in PDB entry 1XK4
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 SER 6 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A THR* 3.5 20.6 - - - -
41A GLU* 2.6 35.7 + - - -
4C LYS 3.4 3.9 + - - -
5C MET* 1.3 76.1 - - - +
7C GLN* 1.3 65.3 + - - +
8C LEU 3.4 1.7 + - - -
9C GLU* 2.9 28.7 + - - +
10C ARG* 2.9 23.9 + - - +
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Residues in contact with GLN 7 (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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11A SER* 2.9 36.6 + - - +
14A ASP* 3.9 16.6 + - - +
15A VAL* 3.7 11.7 - - + -
18A LYS* 2.8 34.7 + - - +
41A GLU* 3.7 1.8 + - - +
6C SER* 1.3 72.6 - - - +
8C LEU* 1.3 63.8 + - - +
10C ARG* 3.2 31.9 + - - +
11C ASN* 3.0 28.5 + - - +
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Residues in contact with LEU 8 (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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12A ILE* 4.1 27.8 - - + -
15A VAL* 4.0 16.7 - - + +
37A LEU* 4.9 3.8 - - + -
41A GLU* 3.2 35.3 + - + +
71A PHE* 4.4 19.5 - - + -
75A VAL* 4.5 14.1 - - + -
78A MET* 3.7 35.2 - - + -
7C GLN* 1.3 78.0 - - - +
9C GLU* 1.3 57.9 + - - +
11C ASN* 3.3 5.4 + - - +
12C ILE* 3.0 35.3 + - + +
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Residues in contact with GLU 9 (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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41A GLU 3.5 7.6 - - - +
42A SER 3.4 2.3 - - - -
43A PRO* 3.0 45.7 - - + +
78A MET* 4.9 3.6 - - + -
4C LYS 4.3 2.4 - - - +
5C MET* 3.6 24.0 - - + +
6C SER* 2.9 41.1 + - - +
8C LEU* 1.3 73.4 - - - +
10C ARG* 1.3 58.8 + - - +
12C ILE* 3.3 7.6 + - - +
13C GLU* 2.8 30.3 + - - +
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Residues in contact with ARG 10 (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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5C MET* 3.3 49.7 + - + -
6C SER 2.9 14.7 + - - +
7C GLN* 3.2 36.7 + - - +
9C GLU* 1.3 75.0 - - - +
11C ASN* 1.3 61.1 + - - +
13C GLU* 3.3 7.9 + - - +
14C THR* 2.9 32.7 + - - +
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Residues in contact with ASN 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ALA* 3.6 25.2 - - + +
11A SER* 2.6 52.8 + - - -
12A ILE* 3.6 16.5 - - + +
15A VAL* 4.3 0.6 - - - +
7C GLN* 3.0 25.4 + - - +
8C LEU* 3.6 8.7 - - - +
9C GLU 3.2 0.2 - - - -
10C ARG* 1.3 77.2 + - - +
12C ILE* 1.3 65.2 + - - +
14C THR* 3.2 4.9 + - - -
15C ILE* 3.1 28.0 + - - +
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Residues in contact with ILE 12 (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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12A ILE* 5.5 0.9 - - + -
75A VAL* 4.3 13.9 - - + +
78A MET* 3.5 44.6 - - + -
79A GLY* 3.9 15.3 - - - +
82A ALA* 3.7 17.0 - - + -
8C LEU* 3.0 30.6 + - + +
9C GLU* 3.8 5.6 - - - +
11C ASN* 1.3 75.4 - - + +
13C GLU* 1.3 56.9 + - - +
15C ILE* 3.1 16.6 + - + +
16C ILE* 2.9 46.5 + - + +
76C PHE* 5.9 0.4 - - + -
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Residues in contact with GLU 13 (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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5C MET* 3.2 36.0 - - - +
9C GLU 2.8 20.5 + - - +
10C ARG* 3.5 8.3 - - - +
12C ILE* 1.3 70.7 - - - +
14C THR* 1.3 67.0 + - - +
16C ILE* 3.2 8.2 + - - +
17C ASN* 2.8 47.0 + - - +
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Residues in contact with THR 14 (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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4A GLU* 3.8 23.6 - - + +
5A LEU* 4.2 3.1 - - - -
8A ALA* 3.7 23.7 - - + +
10C ARG* 2.9 16.4 + - - +
11C ASN* 3.4 9.3 + - - -
13C GLU* 1.3 78.0 - - - +
15C ILE* 1.3 57.2 + - - +
17C ASN* 3.9 4.0 - - - +
18C THR* 2.8 43.6 + - - +
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Residues in contact with ILE 15 (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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5A LEU* 4.0 23.3 - - + -
8A ALA* 4.8 3.8 - - + -
9A LEU* 3.8 23.8 - - + -
12A ILE* 3.9 17.5 - - + -
75A VAL* 5.9 1.8 - - + -
11C ASN 3.1 17.9 + - - +
12C ILE* 3.1 13.9 + - + +
14C THR* 1.3 76.8 - - - +
16C ILE* 1.3 62.6 + - - +
18C THR* 3.8 1.6 - - - -
19C PHE* 3.0 22.9 + - - +
76C PHE* 3.7 25.8 - - + -
79C PHE* 4.2 7.1 - - + -
80C ILE* 4.8 8.3 - - + -
83C MET* 4.1 25.8 - - + -
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Residues in contact with ILE 16 (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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79A GLY 4.1 1.1 - - - +
82A ALA* 3.5 34.1 - - + +
83A HIS* 3.6 24.9 - - + +
86A SER* 3.7 25.6 - - - +
12C ILE* 2.9 26.8 + - + +
13C GLU* 3.2 8.0 + - - +
15C ILE* 1.3 75.5 - - - +
17C ASN* 1.3 67.0 + - - +
19C PHE* 3.4 4.0 + - - +
20C HIS* 2.9 29.8 + - + +
76C PHE* 3.8 25.8 - - + -
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Residues in contact with ASN 17 (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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86A SER* 6.0 0.3 - - - -
13C GLU* 2.8 41.5 + - - +
14C THR* 4.1 3.4 - - - +
16C ILE* 1.3 87.8 - - - +
18C THR* 1.3 58.1 + - - +
20C HIS* 3.8 8.5 - - - +
21C GLN* 3.1 27.0 + - - +
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Residues in contact with THR 18 (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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5A LEU* 4.0 29.3 + - + +
14C THR* 2.8 28.8 + - - +
15C ILE 3.8 3.8 - - - -
17C ASN* 1.3 74.2 - - - +
19C PHE* 1.3 64.1 + - - +
21C GLN* 3.3 9.7 + - - +
22C TYR* 3.2 26.9 - - + -
40C LEU* 4.2 9.4 - - + -
44C ASP* 3.8 32.4 + - + +
79C PHE* 6.1 0.9 - - - -
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Residues in contact with PHE 19 (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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83A HIS* 4.6 3.8 - + - -
15C ILE 3.0 13.2 + - - +
16C ILE 3.5 9.6 - - - +
18C THR* 1.3 74.4 - - - +
20C HIS* 1.3 63.0 + - + +
22C TYR* 3.3 3.3 + - - -
23C SER* 2.9 38.2 + - - -
30C ASP* 3.4 40.4 - - - -
31C THR* 4.0 4.3 - - - -
32C LEU* 3.7 31.2 - - + +
40C LEU* 4.2 10.0 - - - +
74C LEU 3.6 15.0 - - - -
76C PHE* 3.5 46.2 - + + -
79C PHE* 3.7 28.6 - + + -
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Residues in contact with HIS 20 (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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16C ILE* 2.9 20.7 + - + +
17C ASN* 3.8 10.5 - - - +
19C PHE* 1.3 79.3 - - + +
21C GLN* 1.3 70.3 + - - +
22C TYR 3.1 0.7 + - - -
23C SER* 3.4 11.9 + - - -
24C VAL* 3.1 54.4 + - + +
29C PRO* 4.5 4.4 + - + -
30C ASP* 5.4 4.4 + - - +
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Residues in contact with GLN 21 (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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17C ASN 3.1 14.9 + - - +
18C THR* 3.3 13.2 + - - +
20C HIS* 1.3 79.9 - - - +
22C TYR* 1.3 76.7 + - + +
24C VAL* 3.9 7.2 - - - +
25C LYS* 3.4 37.3 - - - +
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Residues in contact with TYR 22 (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 THR* 3.2 18.8 - - + -
19C PHE 3.3 1.5 + - - +
20C HIS 3.0 0.4 - - - -
21C GLN* 1.3 92.3 - - + +
23C SER* 1.3 65.0 + - - +
24C VAL 3.1 3.1 + - - -
25C LYS* 3.2 24.1 + - + +
32C LEU* 3.7 19.1 - - + -
36C GLU* 3.1 28.3 - - + +
39C GLU* 3.5 48.5 - - + -
40C LEU* 3.8 21.5 - - + -
43C LYS* 3.7 26.5 - - - +
44C ASP* 2.7 30.8 + - - -
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Residues in contact with SER 23 (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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19C PHE* 2.9 29.8 + - - -
20C HIS* 3.4 19.3 + - - -
22C TYR* 1.3 73.7 - - - +
24C VAL* 1.3 60.6 + - - +
25C LYS 3.4 1.0 + - - -
26C LEU 3.4 1.6 - - - +
28C HIS 3.2 6.9 - - - +
29C PRO* 2.7 20.8 + - - +
30C ASP* 4.0 1.4 + - - -
31C THR 3.3 30.7 - - - -
32C LEU* 3.6 4.4 - - - +
36C GLU* 3.8 2.0 - - - -
3502C CA 2.3 26.4 - - - -
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Residues in contact with VAL 24 (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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20C HIS* 3.1 47.1 - - + +
21C GLN* 3.9 9.9 - - - +
23C SER* 1.3 80.2 + - - +
25C LYS* 1.3 67.1 + - + +
26C LEU* 3.2 1.5 + - - -
27C GLY 5.7 0.2 - - - +
29C PRO* 3.5 25.1 - - + +
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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
------------------------------------------------------------
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