Contacts of the helix formed by residues 13 - 31 (chain C) in PDB entry 3HJW
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 PRO 13 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11C GLU 3.9 6.1 - - - +
12C VAL* 1.4 89.7 - - + +
14C LYS* 1.3 65.3 + - - +
15C GLU* 4.2 12.3 - - + +
16C LEU* 3.0 25.5 + - + +
17C ALA* 2.9 20.3 + - - +
122C LEU* 5.0 5.6 - - + -
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Residues in contact with LYS 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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12C VAL 3.8 2.0 + - - -
13C PRO* 1.3 70.0 - - - +
15C GLU* 1.3 66.2 + - - +
17C ALA* 3.3 8.3 + - + +
18C GLU* 2.8 38.3 + - + +
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Residues in contact with GLU 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C PRO* 3.2 9.3 - - + +
14C LYS* 1.3 85.0 + - - +
16C LEU* 1.3 57.9 + - - +
18C GLU* 3.3 7.9 + - - +
19C LYS* 3.0 44.6 + - - +
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Residues in contact with LEU 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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12C VAL* 3.9 7.2 - - + -
13C PRO* 3.0 34.2 + - + +
15C GLU* 1.3 75.5 - - - +
17C ALA* 1.3 59.4 + - - +
19C LYS* 3.3 17.7 + - - +
20C ALA* 3.1 25.5 + - - +
79C ILE* 3.7 12.8 - - + -
115C ILE* 4.1 18.4 - - + -
118C LYS* 3.6 38.8 - - + -
119C VAL* 4.3 11.4 - - + -
122C LEU* 4.0 20.6 - - + -
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Residues in contact with ALA 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C VAL* 3.8 16.0 - - + +
13C PRO 2.9 12.0 + - - +
14C LYS* 3.5 12.8 - - + +
16C LEU* 1.3 76.5 - - - +
18C GLU* 1.3 62.4 + - - +
20C ALA* 3.3 6.6 + - - +
21C LEU* 3.2 28.4 + - + +
56C GLU* 5.8 0.9 - - - +
80C TYR 4.3 9.0 - - - +
81C VAL* 3.6 1.5 - - + +
82C PRO* 4.2 25.1 - - + -
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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
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14C LYS* 2.8 23.0 + - + +
15C GLU* 3.6 8.1 - - - +
17C ALA* 1.3 76.3 - - - +
19C LYS* 1.3 59.7 + - + +
21C LEU* 3.4 27.6 + - - +
22C GLN* 3.0 37.9 + - + +
82C PRO* 6.0 0.7 - - - +
86C GLU* 4.3 4.9 - - - +
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Residues in contact with LYS 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C GLU* 3.0 36.4 + - + +
16C LEU* 3.3 26.6 + - - +
18C GLU* 1.3 76.6 - - + +
20C ALA* 1.3 58.2 + - - +
22C GLN* 3.5 5.5 + - - +
23C ALA* 3.0 29.8 + - - +
111C LEU* 3.7 22.2 - - + +
114C GLU* 3.2 36.7 + - - +
115C ILE* 3.6 9.7 - - + +
118C LYS* 3.9 14.5 - - - +
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Residues in contact with ALA 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C LEU 3.1 12.6 + - - +
17C ALA 3.4 10.1 - - - +
18C GLU 3.2 0.4 - - - -
19C LYS* 1.3 77.2 - - - +
21C LEU* 1.3 60.1 + - - +
23C ALA* 3.3 3.5 + - - +
24C VAL* 3.3 29.1 + - - +
51C LEU* 5.5 0.9 - - + -
53C ILE* 4.5 7.1 - - + +
79C ILE* 3.9 28.5 - - + -
81C VAL* 3.9 16.4 - - + -
102C ILE* 5.6 0.2 - - - +
115C ILE* 3.9 10.5 - - + +
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Residues in contact with LEU 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 ALA 3.2 16.0 + - - +
18C GLU* 3.4 26.4 + - - +
20C ALA* 1.3 75.5 - - - +
22C GLN* 1.3 62.5 + - + +
24C VAL* 3.8 2.2 + - - +
25C GLU* 3.4 29.1 + - - +
81C VAL* 3.7 23.6 - - + -
82C PRO* 5.1 2.7 - - + -
86C GLU* 3.2 53.4 - - + +
87C LEU* 4.0 20.0 - - + -
90C ALA* 3.8 12.3 - - + +
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Residues in contact with GLN 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C GLU* 3.0 27.0 + - + +
19C LYS* 3.8 7.9 - - - +
21C LEU* 1.3 77.1 - - + +
23C ALA* 1.3 63.3 + - - +
24C VAL 3.3 0.2 - - - -
25C GLU* 3.2 20.2 + - - +
26C ILE* 3.1 34.1 + - + +
111C LEU* 4.6 7.4 - - + -
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Residues in contact with ALA 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 LYS 3.0 18.6 + - - +
20C ALA 3.6 5.8 - - - +
22C GLN* 1.3 77.2 - - - +
24C VAL* 1.3 57.1 + - - +
26C ILE* 3.6 1.2 + - - +
27C ALA* 3.0 31.6 + - - +
51C LEU* 5.3 0.7 - - + -
102C ILE* 4.4 14.5 - - + +
108C ALA* 4.2 8.4 - - + +
111C LEU* 3.8 19.9 - - + +
112C VAL* 4.6 10.5 - - + +
115C ILE* 4.1 13.5 - - + -
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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 ALA 3.3 16.9 + - - +
21C LEU 4.1 5.2 - - - +
22C GLN 3.3 0.4 - - - -
23C ALA* 1.3 73.2 - - - +
25C GLU* 1.3 65.7 + - - +
27C ALA* 4.2 4.4 - - - +
28C ARG* 3.1 24.1 + - - +
33C ILE* 4.1 12.7 - - + +
53C ILE* 3.8 30.3 - - + -
87C LEU* 4.7 10.3 - - + -
90C ALA* 3.8 25.7 - - + +
91C ALA* 4.2 2.7 - - + +
100C VAL* 3.9 23.6 - - + -
102C ILE* 4.2 7.4 - - + -
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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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21C LEU* 3.4 17.9 + - - +
22C GLN* 3.2 26.1 + - - +
24C VAL* 1.3 79.9 - - - +
26C ILE* 1.3 61.8 + - + +
28C ARG* 3.2 43.2 + - - +
29C ASP* 3.0 21.8 - - - +
89C ALA 3.8 2.9 - - - +
90C ALA* 3.3 25.7 + - - +
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Residues in contact with ILE 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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22C GLN* 3.1 24.7 + - + +
23C ALA 4.0 0.2 - - - +
25C GLU* 1.3 76.5 - - + +
27C ALA* 1.3 63.8 + - - +
28C ARG 3.0 2.8 + - - -
29C ASP* 3.3 8.3 + - - +
30C THR* 2.6 44.8 + - + +
107C LYS* 3.8 20.6 - - + +
108C ALA* 3.8 27.6 - - + -
111C LEU* 4.4 11.7 - - + -
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Residues in contact with ALA 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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23C ALA 3.0 20.4 + - - +
24C VAL 4.2 0.2 - - - +
26C ILE* 1.3 76.1 - - - +
28C ARG* 1.3 56.8 + - - +
30C THR* 4.1 1.3 - - - -
31C GLY 2.9 31.4 + - - -
32C LYS* 3.1 4.9 + - - -
33C ILE* 3.8 18.6 - - + -
102C ILE* 4.3 11.4 - - + -
104C GLU 4.0 7.4 - - - +
105C PRO* 3.4 27.3 + - + +
108C ALA* 5.0 1.1 - - + -
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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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24C VAL 3.1 16.9 + - - +
25C GLU* 3.2 41.4 + - - +
26C ILE 3.0 0.2 + - - -
27C ALA* 1.3 81.4 - - - +
29C ASP* 1.3 72.9 + - - +
31C GLY 3.6 10.0 - - - +
32C LYS* 4.9 1.2 - - - -
33C ILE* 4.0 21.9 + - + +
89C ALA 3.6 3.6 + - - -
90C ALA 3.1 17.8 + - - -
91C ALA 3.4 25.6 - - - +
92C GLY* 3.5 20.1 - - - +
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Residues in contact with ASP 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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25C GLU 3.0 20.0 - - - +
26C ILE* 3.4 11.4 - - - +
28C ARG* 1.3 94.5 + - + +
30C THR* 1.3 78.2 + - - +
31C GLY 3.5 1.5 - - - +
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Residues in contact with THR 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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26C ILE* 2.6 29.2 + - + +
27C ALA* 4.0 0.7 + - - -
29C ASP* 1.3 91.9 - - - +
31C GLY* 1.3 58.0 + - - +
104C GLU* 4.5 3.8 - - - +
106C GLY* 3.5 11.9 - - - -
107C LYS* 3.3 56.8 + - + +
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Residues in contact with GLY 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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27C ALA 2.9 14.9 + - - -
28C ARG 3.6 7.8 - - - +
29C ASP 4.9 1.2 - - - +
30C THR* 1.3 81.2 + - - +
32C LYS* 1.3 62.2 + - - +
104C GLU* 3.4 23.3 - - - -
106C GLY* 4.2 6.7 - - - -
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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