Contacts of the helix formed by residues 14 - 36 (chain C) in PDB entry 2WMZ
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 ASN 14 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A ARG* 4.0 4.5 - - - +
10C ALA 2.7 22.0 + - - +
11C ARG 4.8 0.6 - - - -
13C SER* 1.3 70.3 + - - +
15C PRO* 1.3 66.5 - - - +
16C GLU* 2.9 50.0 + - - +
17C LEU* 3.2 7.8 + - + +
18C ARG* 3.1 23.3 + - - +
105C LEU* 2.8 39.4 - - + +
185C ILE* 3.1 27.6 + - - +
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Residues in contact with PRO 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A GLU* 3.2 32.6 - - - +
317A GLU* 3.5 16.4 - - + -
318A SER* 3.0 34.4 + - - +
321A ARG* 3.4 25.6 - - - +
13C SER 2.8 9.7 - - - +
14C ASN* 1.3 86.0 - - - +
16C GLU* 1.3 70.1 + - - +
18C ARG 4.0 1.1 - - - -
19C LYS* 3.1 26.2 + - - +
184C GLN 5.0 0.2 - - - +
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Residues in contact with GLU 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A SER* 2.6 34.9 + - - +
14C ASN* 2.9 28.9 + - - +
15C PRO* 1.3 84.3 - - - +
17C LEU* 1.3 65.3 + - - +
19C LYS* 3.3 7.4 + - - +
20C SER* 3.0 21.3 + - - -
184C GLN* 5.1 6.6 - - - +
185C ILE* 5.6 0.9 - - - -
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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
----------------------------------------------------------
11C ARG* 4.7 17.7 - - + +
14C ASN* 3.2 13.0 + - + +
16C GLU* 1.3 80.0 - - - +
18C ARG* 1.3 58.3 + - + +
20C SER* 3.4 3.2 + - - -
21C ALA* 3.0 20.3 + - - +
98C TYR* 3.4 26.0 - - + +
101C ASP* 3.2 41.5 - - + +
102C GLN* 3.5 21.5 - - + +
105C LEU* 3.6 34.8 - - + -
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Residues in contact with ARG 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A VAL* 5.2 1.3 - - + +
314A GLU* 2.7 49.6 + - + +
11C ARG 5.4 3.1 + - - +
12C LEU* 3.3 27.0 + - - +
13C SER* 3.5 19.5 + - - +
14C ASN 3.1 18.4 + - - +
15C PRO 4.2 0.2 - - - +
17C LEU* 1.3 77.2 - - + +
19C LYS* 1.3 66.1 + - - +
21C ALA* 2.9 18.5 + - - +
22C ALA* 2.9 15.4 + - - +
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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
----------------------------------------------------------
308A ASN* 5.6 4.9 + - - +
311A GLY* 3.9 19.6 - - - +
312A ALA 5.0 0.2 - - - +
314A GLU* 3.6 11.8 - - + +
315A GLN* 3.5 45.6 + - + +
15C PRO 3.1 18.8 + - - +
16C GLU* 3.5 7.2 - - - +
18C ARG* 1.3 77.8 - - - +
20C SER* 1.3 63.4 + - - +
22C ALA* 3.4 2.9 + - - +
23C ASP* 3.1 51.1 + - - +
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Residues in contact with SER 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C GLU 3.0 13.1 + - - -
17C LEU 3.5 9.6 - - - -
18C ARG 3.1 0.4 - - - -
19C LYS* 1.3 76.7 - - - +
21C ALA* 1.3 63.3 + - - +
23C ASP* 3.3 11.4 + - - +
24C ARG* 3.2 17.7 + - - +
94C GLN* 4.0 3.6 + - - +
97C THR* 4.6 2.1 - - - +
98C TYR* 3.1 23.8 + - - -
101C ASP* 2.8 36.0 + - - -
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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
----------------------------------------------------------
17C LEU 3.0 8.8 + - - +
18C ARG* 2.9 14.0 + - - +
20C SER* 1.3 72.5 - - - +
22C ALA* 1.3 58.1 + - - +
23C ASP 3.0 0.9 - - - -
24C ARG* 2.8 33.3 + - - +
25C ASP* 2.9 21.4 + - - +
98C TYR* 3.5 29.4 - - + +
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Residues in contact with ALA 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A TYR* 3.4 31.2 - - + +
308A ASN* 5.5 0.6 - - - -
310A VAL* 3.8 15.3 - - + -
311A GLY* 3.7 16.4 - - - +
18C ARG 2.9 10.6 + - - +
19C LYS 3.7 8.1 - - - +
21C ALA* 1.3 75.1 - - - +
23C ASP* 1.3 59.2 + - - +
25C ASP* 3.8 11.4 + - - -
26C ALA* 3.1 27.2 + - - +
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Residues in contact with ASP 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A TYR 5.7 0.2 - - - +
308A ASN* 5.7 3.6 - - - -
311A GLY* 5.2 0.7 - - - -
19C LYS* 3.1 52.8 + - - +
20C SER* 3.5 11.8 - - - +
21C ALA 3.0 1.4 - - - -
22C ALA* 1.3 79.2 - - - +
24C ARG* 1.3 64.5 + - - +
26C ALA* 3.7 5.6 + - - +
27C ALA* 3.2 21.5 + - - +
94C GLN* 3.6 19.0 + - - +
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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
----------------------------------------------------------
20C SER 3.2 11.5 + - - +
21C ALA* 2.8 18.4 + - - +
23C ASP* 1.3 75.4 - - - +
25C ASP* 1.3 91.5 + - - +
27C ALA* 3.3 1.0 + - - +
28C PHE* 3.0 44.5 + - + -
94C GLN* 3.3 14.6 - - + +
95C ASP* 3.0 32.3 + - - +
98C TYR* 3.5 40.6 + - + -
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Residues in contact with ASP 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A TYR* 3.5 42.6 - - + -
21C ALA* 2.9 16.2 + - - +
22C ALA* 3.7 9.8 + - - +
23C ASP 3.3 0.2 - - - -
24C ARG* 1.3 106.7 + - - +
26C ALA* 1.3 65.7 + - - +
28C PHE* 3.2 5.0 + - - +
29C GLU* 2.9 24.6 + - - +
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Residues in contact with ALA 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A GLN* 3.9 18.5 - - + +
307A TYR* 3.5 21.2 - - + -
308A ASN* 4.9 5.6 - - + +
22C ALA 3.1 18.0 + - - +
23C ASP* 4.0 6.1 - - - +
25C ASP* 1.3 74.8 - - - +
27C ALA* 1.3 55.4 + - - +
29C GLU* 3.1 3.8 + - - +
30C LYS* 2.8 36.4 + - - +
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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
----------------------------------------------------------
23C ASP 3.2 13.1 + - - +
24C ARG 3.4 9.2 - - - +
25C ASP 3.2 0.2 - - - -
26C ALA* 1.3 79.4 - - - +
28C PHE* 1.3 59.7 + - - +
30C LYS* 3.6 3.7 - - - +
31C ILE* 3.9 1.7 + - - +
87C GLN* 3.1 25.4 - - - +
90C ALA* 5.0 1.3 - - + +
91C ALA* 3.5 18.3 - - - +
94C GLN* 3.6 26.5 - - + +
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Residues in contact with PHE 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ARG* 3.0 48.9 + - + +
25C ASP* 3.9 3.8 - - - +
27C ALA* 1.3 72.4 - - - +
29C GLU* 1.3 68.1 + - - +
30C LYS 3.0 2.0 - - - -
31C ILE* 2.9 33.7 + - + +
32C ASN* 4.2 1.9 + - - -
88C GLU 5.6 0.7 - - - -
91C ALA* 3.0 45.1 - - + -
92C GLY* 4.1 4.0 - - - -
95C ASP* 4.1 15.7 - - + -
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Residues in contact with GLU 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A SER* 2.8 48.2 + - - +
303A LYS* 3.0 48.6 + - + +
304A GLN* 3.7 6.1 - - + +
307A TYR* 3.7 15.7 + - + -
25C ASP 2.9 17.5 + - - +
26C ALA 3.6 3.4 - - - +
28C PHE* 1.3 77.7 - - - +
30C LYS* 1.3 59.8 + - - +
32C ASN* 2.9 32.9 + - - +
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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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304A GLN* 2.9 36.2 + - - +
26C ALA 2.8 16.4 + - - +
27C ALA* 3.6 2.0 - - - +
28C PHE 3.0 0.2 - - - -
29C GLU* 1.3 73.4 - - - +
31C ILE* 1.3 61.7 + - - +
32C ASN 2.8 7.2 + - - -
33C GLU* 2.9 38.0 + - + +
34C ALA* 3.0 10.3 + - + +
87C GLN* 2.9 38.6 - - + +
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Residues in contact with ILE 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 4.0 4.7 - - - +
28C PHE* 2.9 29.3 + - + +
30C LYS* 1.3 77.2 - - - +
32C ASN* 1.3 62.0 + - - +
34C ALA 3.4 0.6 + - - -
35C ARG* 3.1 29.6 + - - +
84C LEU* 3.3 12.8 - - + +
87C GLN* 3.4 25.8 - - + +
88C GLU* 3.6 44.4 - - + +
91C ALA* 3.7 15.3 - - + -
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Residues in contact with ASN 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A GLY 4.8 1.0 - - - +
296A GLY* 5.7 1.8 - - - +
297A MET 5.8 0.2 - - - -
300A SER* 3.0 19.3 - - - +
303A LYS* 5.3 1.6 + - - +
28C PHE 5.2 1.5 + - - -
29C GLU* 2.9 28.9 + - - +
30C LYS 2.8 1.2 + - - -
31C ILE* 1.3 77.1 - - - +
33C GLU* 1.3 53.3 + - - +
34C ALA 2.8 4.3 - - - -
35C ARG* 2.8 36.6 + - - +
36C SER* 2.7 34.9 + - - -
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Residues in contact with GLU 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A MET* 4.3 13.8 - - + +
300A SER* 2.7 26.1 + - - +
301A GLN* 3.4 34.5 - - + +
304A GLN* 2.6 30.1 + - - +
30C LYS* 2.9 30.2 + - + +
32C ASN* 1.3 73.1 - - - +
34C ALA* 1.3 58.6 + - - +
36C SER* 3.2 19.6 - - - -
37C PRO* 3.2 9.0 - - - +
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Residues in contact with ALA 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 5.1 + - + +
31C ILE 3.4 9.0 - - - +
32C ASN 2.8 0.8 + - - -
33C GLU* 1.3 77.7 - - - +
35C ARG* 1.3 61.2 + - - +
37C PRO* 3.3 10.9 - - - +
38C LEU* 5.3 0.2 - - - +
80C LYS 4.2 7.1 - - - +
83C ALA* 4.1 8.0 - - + +
84C LEU* 3.7 24.2 + - + +
87C GLN* 3.3 37.0 - - + +
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Residues in contact with ARG 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A GLY 5.7 1.8 + - - -
31C ILE* 3.1 17.1 + - - +
32C ASN* 2.8 42.7 + - - +
34C ALA* 1.3 74.9 - - - +
36C SER* 1.3 55.2 + - - +
37C PRO 3.2 0.9 - - - -
38C LEU* 2.6 43.2 + - + +
39C LEU* 3.9 19.7 + - + +
84C LEU* 3.4 35.8 - - + +
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Residues in contact with SER 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A GLN 2.9 9.0 + - - -
295A GLY* 2.9 34.1 - - - -
297A MET* 2.8 39.0 - - - +
32C ASN 2.7 14.7 + - - -
33C GLU 3.2 13.2 - - - -
35C ARG* 1.3 71.2 - - - +
37C PRO* 1.3 65.1 - - - +
39C LEU* 2.9 19.5 + - - +
41C GLN* 3.4 3.3 + - - +
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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
------------------------------------------------------------
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