Contacts of the helix formed by residues 18 - 39 (chain C) in PDB entry 3DH1
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 18 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C PHE 3.4 2.5 + - - -
17C GLN* 1.3 73.6 - - - +
19C MET* 1.3 53.9 + - - +
20C GLU* 3.4 7.2 + - - +
21C GLU* 2.8 43.5 + - - +
22C THR* 2.6 36.4 + - - -
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Residues in contact with MET 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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18C SER* 1.3 71.9 - - - +
20C GLU* 1.3 66.7 + - + +
22C THR* 3.4 14.2 - - + -
23C GLU* 3.2 36.9 + - + +
155C ILE* 6.2 4.5 - - - -
158C TYR* 5.8 6.1 - - + -
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Residues in contact with GLU 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C SER* 3.3 7.0 + - - +
19C MET* 1.3 76.7 - - + +
21C GLU* 1.3 67.6 + - + +
23C GLU* 3.3 19.6 + - - +
24C LYS* 3.0 21.0 + - - +
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Residues in contact with GLU 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C TYR* 2.7 30.3 + - - -
16C PHE 4.0 0.2 - - - +
17C GLN* 3.3 28.4 - - + +
18C SER* 2.8 48.9 + - - +
20C GLU* 1.3 78.4 - - + +
22C THR* 1.3 56.6 + - - +
24C LYS* 3.2 21.9 + - - +
25C TRP* 2.9 34.6 + - - +
52C ASN* 4.5 4.6 + - - +
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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
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17C GLN* 4.3 8.9 + - - +
18C SER 2.6 21.0 + - - -
19C MET* 3.4 20.5 - - + -
21C GLU* 1.3 73.6 - - - +
23C GLU* 1.3 54.2 + - - +
25C TRP* 3.0 6.0 + - - +
26C MET* 2.8 36.9 + - + +
101C TYR* 3.3 35.2 + - + -
123C VAL* 4.0 25.6 - - + -
158C TYR* 6.4 0.4 - - + -
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Residues in contact with GLU 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C MET* 3.2 29.7 + - + +
20C GLU* 3.3 20.8 - - - +
22C THR* 1.3 78.5 - - - +
24C LYS* 1.3 62.1 + - - +
26C MET* 3.3 1.7 + - - +
27C GLU* 2.9 31.6 + - - +
158C TYR* 3.5 41.6 + - + +
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Residues in contact with LYS 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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17C GLN* 5.2 0.4 + - - -
20C GLU 3.0 12.7 + - - +
21C GLU* 3.2 24.4 + - - +
23C GLU* 1.3 76.5 - - - +
25C TRP* 1.3 105.0 + - + +
27C GLU* 3.5 16.3 + - - +
28C GLU* 3.3 24.3 + - - +
52C ASN* 5.5 2.2 + - - -
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Residues in contact with TRP 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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17C GLN* 3.2 25.1 + - + -
21C GLU 2.9 21.0 + - - -
22C THR 3.0 4.7 + - - +
24C LYS* 1.3 112.3 - - + +
26C MET* 1.3 65.0 + - - +
28C GLU* 3.2 19.3 + - - -
29C ALA* 3.0 19.1 + - - +
47C LEU* 3.2 20.1 - - + +
49C VAL* 3.4 27.9 - - + +
52C ASN* 4.9 9.0 - - - -
54C VAL* 3.5 30.1 - - + -
101C TYR* 3.5 48.2 - + + -
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Residues in contact with MET 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C THR* 2.8 23.2 + - + +
23C GLU 3.8 0.4 - - - +
25C TRP* 1.3 69.3 - - - +
27C GLU* 1.3 66.6 + - - +
29C ALA* 3.1 7.0 + - - +
30C MET* 2.9 29.0 + - + +
101C TYR* 3.7 23.6 - - + -
102C VAL 3.5 24.0 - - - +
103C THR* 5.2 1.6 - - - -
123C VAL* 3.6 28.9 - - + +
124C TYR* 3.5 24.9 - - - +
125C GLY* 3.8 2.5 - - - +
158C TYR* 3.4 46.2 - - + +
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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
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23C GLU* 2.9 20.4 + - - +
24C LYS* 3.5 19.6 - - - +
26C MET* 1.3 74.0 - - - +
28C GLU* 1.3 59.5 + - - +
30C MET* 3.0 19.3 + - - +
31C HIS* 3.1 26.1 + - + +
158C TYR* 4.9 3.7 - - - +
159C ARG* 3.1 30.1 + - - +
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Residues in contact with GLU 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 LYS* 3.3 13.0 + - - +
25C TRP* 3.2 29.9 + - - +
27C GLU* 1.3 79.8 - - - +
29C ALA* 1.3 55.9 + - - +
31C HIS* 3.3 13.4 + - + +
32C MET* 3.1 31.3 + - + +
47C LEU* 3.7 13.9 - - + +
54C VAL* 5.1 1.6 - - - +
57C LYS* 3.2 27.5 + - - +
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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
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25C TRP 3.0 12.7 + - - +
26C MET* 3.1 13.0 + - - +
28C GLU* 1.3 76.4 - - - +
30C MET* 1.3 57.1 + - - +
32C MET* 3.6 5.3 + - - -
33C ALA* 3.0 19.9 + - - +
45C GLY* 3.5 26.6 - - - +
46C CYS* 4.2 0.4 - - - +
47C LEU* 3.6 11.1 - - + +
101C TYR 4.0 16.6 - - - +
102C VAL 5.0 0.7 - - - -
103C THR* 3.2 15.8 + - - +
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Residues in contact with MET 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C MET* 2.9 20.2 + - + +
27C GLU* 3.2 10.1 - - - +
29C ALA* 1.3 76.7 - - - +
31C HIS* 1.3 59.6 + - + +
32C MET 3.3 0.4 - - - -
33C ALA* 3.4 4.7 + - - +
34C LYS* 3.0 44.8 + - - +
103C THR* 4.2 17.9 - - - +
158C TYR* 6.1 0.7 - - + +
159C ARG* 4.2 29.2 - - + +
162C GLU* 3.4 39.5 - - + +
163C ALA* 4.2 7.2 - - - +
166C MET* 3.5 30.7 - - + +
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Residues in contact with HIS 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C GLU* 3.1 23.3 + - + +
28C GLU* 3.3 17.0 + - + +
30C MET* 1.3 76.7 - - - +
32C MET* 1.3 64.1 + - + +
34C LYS* 3.0 34.1 + - - +
35C GLU* 3.1 26.0 + - - +
159C ARG* 6.4 0.2 - - - -
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Residues in contact with MET 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C GLU* 3.1 24.4 + - + +
29C ALA* 3.7 6.3 - - - +
31C HIS* 1.3 77.6 - - + +
33C ALA* 1.3 56.5 + - - +
35C GLU* 3.2 15.5 + - - +
36C ALA 3.0 22.7 + - - -
45C GLY* 4.0 5.6 - - - -
46C CYS 4.1 16.2 - - - +
47C LEU* 4.7 7.2 - - - -
57C LYS* 4.3 24.9 - - + -
58C GLY* 3.4 35.4 - - - +
59C ARG* 3.1 49.0 - - + +
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Residues in contact with ALA 33 (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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29C ALA 3.0 18.7 + - - +
30C MET* 3.5 7.9 - - - +
32C MET* 1.3 72.7 - - - +
34C LYS* 1.3 64.6 + - - +
36C ALA* 3.3 1.5 + - - +
37C LEU 3.0 19.2 + - - -
43C PRO* 3.4 28.0 - - - +
44C VAL 4.3 1.1 - - - +
45C GLY* 3.9 13.8 - - - +
103C THR* 3.8 14.1 - - + +
166C MET* 4.1 14.6 - - + -
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Residues in contact with LYS 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 MET* 3.0 33.8 + - - +
31C HIS* 3.0 43.5 + - - +
33C ALA* 1.3 74.1 - - - +
35C GLU* 1.3 60.7 + - + +
37C LEU* 3.3 15.5 - - + +
38C GLU* 2.7 40.0 + - - +
159C ARG* 5.4 4.9 - - - +
166C MET* 4.1 18.7 - - + -
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Residues in contact with GLU 35 (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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31C HIS* 3.1 16.1 + - - +
32C MET* 3.3 19.3 - - - +
33C ALA 3.1 0.2 - - - -
34C LYS* 1.3 75.3 - - + +
36C ALA* 1.3 63.8 + - - +
38C GLU* 3.2 18.1 + - - +
39C ASN* 3.3 23.4 + - - +
59C ARG* 2.6 40.3 + - - +
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Residues in contact with ALA 36 (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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32C MET 3.0 12.6 + - - +
33C ALA 3.6 7.6 - - - +
35C GLU* 1.3 74.0 - - - +
37C LEU* 1.3 63.0 + - - +
39C ASN* 3.3 10.6 + - - +
41C GLU* 2.9 38.5 + - + +
42C VAL 3.3 23.8 - - - +
43C PRO* 3.7 3.4 - - + -
44C VAL 4.0 4.0 - - - +
59C ARG* 3.9 22.5 - - + +
60C ASN 4.8 0.2 - - - +
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Residues in contact with LEU 37 (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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33C ALA 3.0 13.3 + - - +
34C LYS* 3.3 17.0 - - + +
35C GLU 3.2 0.2 - - - -
36C ALA* 1.3 78.8 - - - +
38C GLU* 1.3 65.1 + - + +
39C ASN 3.3 0.2 - - - -
40C THR* 3.4 12.5 + - - -
41C GLU 3.9 5.8 + - - +
43C PRO* 4.0 15.1 - - + +
166C MET* 4.1 22.0 - - + +
169C THR* 4.3 18.2 - - + -
170C PHE* 4.0 32.2 - - + -
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Residues in contact with GLU 38 (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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34C LYS* 2.7 34.4 + - - +
35C GLU* 3.2 10.6 + - - +
37C LEU* 1.3 82.4 - - + +
39C ASN* 1.3 62.8 + - - +
40C THR* 3.4 3.6 + - - -
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Residues in contact with ASN 39 (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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35C GLU* 3.3 25.2 + - - +
36C ALA* 3.3 7.0 + - - +
38C GLU* 1.3 83.2 - - - +
40C THR* 1.3 69.9 + - - +
41C GLU* 3.1 14.0 + - + +
59C ARG* 5.1 8.3 - - - +
63C ASN* 5.1 2.6 + - - +
64C GLN* 3.9 28.3 + - - +
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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
------------------------------------------------------------
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