Contacts of the helix formed by residues 14 - 32 (chain C) in PDB entry 3W1Y
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 ASP 14 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C ALA* 3.6 11.2 - - - +
13C PHE* 1.3 79.8 - - + +
15C HIS* 1.3 66.8 + - - +
16C ARG* 2.8 50.1 + - - +
17C LEU* 3.4 34.4 + - + +
18C ILE 3.2 15.4 + - - -
70C HIS* 4.3 1.1 - - - -
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Residues in contact with HIS 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C PHE 3.9 0.4 + - - -
14C ASP* 1.3 74.9 + - - +
16C ARG* 1.3 77.8 + - + +
17C LEU 3.5 0.2 - - - -
18C ILE* 3.3 11.3 - - + +
19C ASP* 3.1 51.8 + - - +
70C HIS* 3.6 41.6 + + + +
72C ARG* 4.6 5.6 - - - +
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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
----------------------------------------------------------
14C ASP* 2.8 32.0 + - - +
15C HIS* 1.3 98.1 - - + +
17C LEU* 1.3 66.8 + - + +
19C ASP* 3.6 3.7 + - - +
20C GLN* 3.2 23.2 + - - +
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Residues in contact with LEU 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ALA* 5.0 0.4 - - + -
14C ASP* 3.4 34.2 + - + +
16C ARG* 1.3 80.2 - - + +
18C ILE* 1.3 57.1 + - - +
20C GLN* 3.3 12.6 + - - +
21C ALA* 2.9 31.2 + - - +
93C ALA* 4.3 17.0 - - + -
95C GLY* 4.3 27.1 - - - +
96C VAL* 3.7 15.8 - - + +
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Residues in contact with ILE 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C LEU* 3.4 36.8 - - + +
11C LYS* 3.8 3.1 - - - -
12C ALA* 3.9 17.3 - - + +
14C ASP 3.2 5.1 + - - +
15C HIS* 3.3 21.5 - - - +
16C ARG 3.3 0.2 - - - -
17C LEU* 1.3 77.8 - - - +
19C ASP* 1.3 58.0 + - - +
21C ALA* 3.9 0.9 - - - +
22C THR* 2.5 37.6 + - - -
70C HIS* 3.3 35.9 - - + +
72C ARG* 3.8 36.8 - - + +
96C VAL* 4.1 9.1 - - + +
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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
----------------------------------------------------------
15C HIS* 3.1 39.3 + - - +
16C ARG* 4.2 3.8 - - - +
18C ILE* 1.3 75.8 - - - +
20C GLN* 1.3 58.6 + - - +
22C THR* 3.9 5.0 - - - -
23C ALA* 3.0 27.5 + - - +
72C ARG* 3.0 34.7 + - - -
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Residues in contact with GLN 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ARG 3.2 17.8 + - - +
17C LEU* 3.8 14.2 - - - +
18C ILE 3.3 0.2 - - - -
19C ASP* 1.3 75.8 - - - +
21C ALA* 1.3 63.3 + - - +
23C ALA* 3.4 5.9 + - - +
24C GLU* 2.9 57.8 + - - +
91C ASP 5.4 1.2 + - - -
92C LEU* 5.4 0.4 - - - +
93C ALA* 4.3 19.1 - - - +
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Residues in contact with ALA 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C LEU* 4.0 18.2 - - + -
17C LEU 2.9 17.8 + - - +
18C ILE 3.9 3.1 - - - +
20C GLN* 1.3 83.1 - - - +
22C THR* 1.3 60.7 + - - +
24C GLU* 3.3 4.9 + - - +
25C ILE* 3.0 33.1 + - - +
92C LEU* 4.3 16.4 - - + +
93C ALA 5.5 2.2 - - - +
96C VAL* 4.0 18.4 - - + -
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Residues in contact with THR 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C LEU* 4.0 12.5 - - + +
18C ILE 2.5 25.4 + - - -
19C ASP* 3.9 8.1 - - - -
21C ALA* 1.3 72.8 - - - +
23C ALA* 1.3 65.7 + - - +
25C ILE* 3.2 5.8 + - - +
26C VAL* 3.0 27.5 + - - +
39C PRO* 3.4 38.1 - - + -
72C ARG* 3.5 26.3 - - + +
74C VAL* 3.8 17.0 - - + -
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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
----------------------------------------------------------
19C ASP 3.0 18.9 + - - +
20C GLN* 3.8 5.8 - - - +
22C THR* 1.3 75.7 - - - +
24C GLU* 1.3 62.8 + - - +
26C VAL* 3.8 6.5 - - - +
27C GLU* 3.0 27.6 + - - +
39C PRO* 5.4 1.8 - - - +
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Residues in contact with GLU 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C GLN* 2.9 38.9 + - - +
21C ALA* 3.6 6.3 - - - +
22C THR 3.2 0.2 - - - -
23C ALA* 1.3 78.2 - - - +
25C ILE* 1.3 56.7 + - - +
27C GLU* 3.8 13.1 - - - +
28C THR* 2.7 34.5 + - - +
31C ARG* 6.1 0.4 - - - +
90C LEU* 3.9 25.3 - - + +
91C ASP* 3.9 13.6 + - - +
92C LEU* 3.5 17.1 - - + +
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Residues in contact with ILE 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ILE* 3.6 43.1 - - + -
10C LEU* 3.7 32.8 - - + -
21C ALA 3.0 14.7 + - - +
22C THR* 3.2 5.1 + - - +
24C GLU* 1.3 72.9 - - - +
26C VAL* 1.3 65.3 + - - +
28C THR* 3.4 2.6 + - - -
29C ALA* 3.0 22.2 + - - +
74C VAL* 4.2 15.9 - - + -
76C ILE* 4.5 2.5 - - + -
87C LEU* 4.4 10.4 - - + +
90C LEU* 3.9 21.8 - - + -
92C LEU* 4.1 18.2 - - + -
98C VAL* 4.7 2.9 - - + -
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Residues in contact with VAL 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C THR 3.0 21.2 + - - +
23C ALA* 3.8 6.5 - - - +
25C ILE* 1.3 76.2 - - - +
27C GLU* 1.3 64.6 + - - +
29C ALA* 3.1 6.6 + - - +
30C LYS* 2.9 52.6 + - + +
36C VAL* 4.0 22.8 - - + +
38C GLY 5.0 2.9 - - - +
39C PRO* 3.9 31.6 - - + -
74C VAL* 4.3 9.9 - - + -
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Residues in contact with GLU 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ALA 3.0 18.2 + - - +
24C GLU* 3.8 13.9 - - - +
26C VAL* 1.3 77.2 - - - +
28C THR* 1.3 52.4 + - - +
30C LYS* 3.1 8.4 + - - +
31C ARG* 2.5 77.4 + - + +
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Residues in contact with THR 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C GLU* 2.7 22.5 + - - +
25C ILE 3.6 4.9 - - - -
26C VAL 3.3 0.2 - - - -
27C GLU* 1.3 72.9 - - - +
29C ALA* 1.3 65.2 + - - +
31C ARG* 3.1 28.4 + - - +
32C THR* 3.2 29.8 + - - +
83C THR 5.1 0.7 - - - +
86C ALA* 3.6 39.3 - - + +
87C LEU* 4.4 7.4 - - + -
90C LEU* 3.5 24.6 - - + +
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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
----------------------------------------------------------
25C ILE 3.0 14.0 + - - +
26C VAL* 3.4 8.3 - - - +
28C THR* 1.3 75.8 - - - +
30C LYS* 1.3 60.3 + - - +
32C THR* 2.9 20.2 + - - -
34C ALA* 3.0 21.5 + - + +
36C VAL* 3.5 20.6 - - + -
76C ILE* 3.9 31.0 - - + -
83C THR* 4.5 5.6 - - - -
87C LEU* 5.3 0.8 - - + +
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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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26C VAL* 2.9 37.5 + - + +
27C GLU* 3.1 10.1 + - - +
29C ALA* 1.3 75.2 - - - +
31C ARG* 1.3 64.3 + - + +
33C GLY* 3.1 13.5 + - - -
34C ALA 4.2 10.7 - - - +
36C VAL* 4.0 25.8 + - + +
38C GLY 5.2 5.1 + - - -
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Residues in contact with ARG 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C GLU* 6.1 0.4 - - - +
27C GLU* 2.5 51.5 + - + +
28C THR* 3.1 39.8 + - - +
29C ALA 3.4 0.2 - - - -
30C LYS* 1.3 72.9 - - + +
32C THR* 1.3 62.5 + - - +
33C GLY 3.3 1.2 + - - -
86C ALA* 5.7 2.0 - - - +
90C LEU* 5.4 2.6 - - - +
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Residues in contact with THR 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C THR* 3.2 16.0 + - + +
29C ALA* 2.9 13.2 + - - -
31C ARG* 1.3 83.3 - - + +
33C GLY* 1.3 59.1 + - - +
80C THR* 3.1 21.5 + - - +
82C LYS* 3.6 29.1 - - + +
83C THR* 2.6 34.1 + - - -
86C ALA* 3.9 13.5 - - + -
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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
------------------------------------------------------------
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