Contacts of the helix formed by residues 12 - 27 (chain C) in PDB entry 5XAC
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 12 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11C ARG* 1.3 76.5 - - - +
13C PHE* 1.3 65.8 + - - +
14C GLU* 3.6 11.1 + - - +
15C GLN* 3.0 40.8 + - - +
16C ARG* 2.9 23.6 + - - +
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Residues in contact with PHE 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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12C THR* 1.3 73.6 - - - +
14C GLU* 1.3 62.4 + - + +
16C ARG* 3.2 25.4 + - - +
17C VAL* 2.9 52.3 + - + +
104C ASP* 4.9 1.6 - - - -
105C GLU* 3.9 20.6 - - + -
106C ASP* 3.7 32.8 - - + -
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Residues in contact with GLU 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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72A GLN* 5.1 11.5 + - - +
12C THR* 3.3 9.5 + - - +
13C PHE* 1.3 84.5 - - + +
15C GLN* 1.3 67.4 + - + +
17C VAL* 3.5 7.2 + - - +
18C GLU* 3.2 22.9 + - - +
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Residues in contact with GLN 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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10C ARG 4.6 1.6 - - - +
11C ARG* 3.5 43.0 + - + +
12C THR* 3.0 46.5 + - - +
14C GLU* 1.3 82.0 - - + +
16C ARG* 1.3 57.5 + - - +
18C GLU* 3.3 5.6 + - - +
19C ASP* 2.9 34.4 + - - +
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Residues in contact with ARG 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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7C PHE* 3.6 24.7 - - + -
8C LYS* 3.6 36.0 + - - +
11C ARG* 3.0 32.6 + - + -
12C THR* 2.9 10.8 + - - +
13C PHE* 3.4 39.7 - - - +
15C GLN* 1.3 72.6 - - - +
17C VAL* 1.3 66.0 + - - +
19C ASP* 3.3 8.7 + - - +
20C VAL* 3.0 27.5 + - - +
104C ASP* 4.6 1.2 + - - -
106C ASP* 2.8 47.9 + - + +
108C PHE* 4.0 3.6 - - + -
110C TYR* 3.5 11.2 - - - -
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Residues in contact with VAL 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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13C PHE* 2.9 52.1 + - + +
14C GLU* 3.8 6.7 - - - +
16C ARG* 1.3 77.3 - - - +
18C GLU* 1.3 57.9 + - - +
20C VAL* 3.3 2.6 + - - +
21C ARG* 3.0 45.7 + - + +
105C GLU 4.7 1.3 - - - +
106C ASP* 3.7 20.9 - - - +
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Residues in contact with GLU 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ASP* 2.8 32.2 - - - +
14C GLU 3.2 14.7 + - - +
15C GLN* 3.9 4.9 - - - +
17C VAL* 1.3 75.8 - - - +
19C ASP* 1.3 70.1 + - - +
21C ARG* 2.8 45.9 + - - +
22C LEU* 3.0 43.8 + - + +
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Residues in contact with ASP 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C PHE* 4.4 5.7 - - - -
11C ARG* 2.9 40.1 + - - -
15C GLN 2.9 22.7 + - - +
16C ARG* 3.4 10.8 - - - +
18C GLU* 1.3 80.1 - - - +
20C VAL* 1.3 62.7 + - - +
22C LEU* 3.3 4.7 + - - +
23C ILE* 3.1 32.1 + - + +
51C LYS* 5.1 6.7 + - - +
108C PHE* 3.9 14.6 - - + -
-3D PHE* 5.7 2.7 - - + -
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Residues in contact with VAL 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 ARG 3.0 12.6 + - - +
17C VAL 3.8 1.8 - - - +
19C ASP* 1.3 73.4 - - - +
21C ARG* 1.3 69.8 + - - +
23C ILE* 3.4 5.8 - - - +
24C ARG* 2.9 45.3 + - + +
32C PRO* 4.5 4.0 - - + -
99C TYR* 4.1 2.7 - - - +
106C ASP 3.6 7.4 - - - +
107C GLY* 3.6 32.1 - - - +
108C PHE* 3.4 46.9 - - + +
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Residues in contact with ARG 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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48A ASP* 4.8 0.9 - - - -
69A ARG* 3.8 28.7 - - - +
70A ARG* 4.3 15.7 - - - +
72A GLN* 6.0 2.4 - - - +
17C VAL* 3.0 29.4 + - + +
18C GLU* 2.8 48.4 + - - +
20C VAL* 1.3 77.8 - - - +
22C LEU* 1.3 64.5 + - - +
24C ARG* 3.4 4.6 + - - +
25C GLU* 2.9 49.7 + - + +
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Residues in contact with LEU 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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48A ASP* 3.7 8.5 - - + +
49A LYS* 3.6 36.3 - - + +
70A ARG* 3.6 27.6 - - - +
-2B VAL* 4.3 2.0 - - + -
18C GLU* 3.0 38.1 + - + +
19C ASP* 3.8 5.6 - - - +
21C ARG* 1.3 77.2 - - - +
23C ILE* 1.3 65.7 + - + +
25C GLU* 3.1 6.1 + - - +
26C GLN* 2.9 41.8 + - - +
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Residues in contact with ILE 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 ASP* 3.1 18.4 + - - +
20C VAL* 3.4 14.1 - - - +
22C LEU* 1.3 78.4 - - + +
24C ARG* 1.3 67.6 + - + +
26C GLN* 4.5 4.0 - - - +
27C HIS* 2.7 43.6 + - + +
30C LYS 4.6 3.1 - - - +
32C PRO* 3.4 41.3 - - + -
53C LEU* 3.7 20.4 - - + -
-3D PHE* 3.6 30.1 - - + -
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Residues in contact with ARG 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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40B GLY 5.7 0.8 + - - -
42B LYS* 3.8 41.9 + - - +
20C VAL* 2.9 35.8 + - + +
21C ARG* 3.9 4.3 - - - +
23C ILE* 1.3 78.9 - - + +
25C GLU* 1.3 62.4 + - + +
27C HIS 4.2 2.9 - - - -
28C PRO* 3.3 42.3 + - - +
30C LYS 3.2 26.9 + - - -
31C ILE* 3.9 13.9 - - - +
32C PRO* 4.0 13.2 - - - -
56C ASP* 4.8 1.4 + - - -
99C TYR* 3.8 29.7 + - - +
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Residues in contact with GLU 25 (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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70A ARG* 2.8 44.6 + - - -
-3B PHE 3.8 1.0 - - - +
-2B VAL* 3.4 19.1 - - + +
-1B THR* 3.1 44.3 + - - +
0B ILE* 5.0 1.6 - - - +
1B GLU* 6.0 3.7 - - + +
42B LYS* 6.1 0.7 - - - +
21C ARG* 2.9 37.9 + - + +
22C LEU* 3.7 7.5 - - - +
24C ARG* 1.3 77.9 - - + +
26C GLN* 1.3 62.0 + - - +
28C PRO* 4.6 4.0 - - - +
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Residues in contact with GLN 26 (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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49A LYS* 3.8 31.3 + - - +
-4B ASP* 3.2 40.9 - - + +
-3B PHE 3.5 20.2 - - - +
-2B VAL* 4.2 7.6 - - + -
22C LEU* 2.9 36.5 + - - +
23C ILE* 5.0 2.0 - - - -
25C GLU* 1.3 80.8 - - - +
27C HIS* 1.3 78.7 + - - +
28C PRO* 3.7 6.9 - - - +
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Residues in contact with HIS 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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-4B ASP* 4.2 13.2 + - + -
23C ILE* 2.7 28.8 + - + +
24C ARG* 3.7 3.4 - - - +
26C GLN* 1.3 99.0 + - + +
28C PRO* 1.3 67.5 - - - +
29C THR* 3.1 4.1 + - - -
30C LYS* 3.1 52.7 + - + +
53C LEU* 4.0 21.9 - - + +
-1D THR* 5.6 2.3 + - - -
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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