Contacts of the helix formed by residues 18 - 39 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A PHE 3.5 1.0 + - - -
17A GLN* 1.3 72.1 - - - +
19A MET* 1.3 60.3 + - - +
20A GLU* 3.4 7.5 + - - +
21A GLU* 2.7 38.0 + - - +
22A THR* 2.9 32.1 + - - -
155B ILE* 4.0 2.0 - - - -
156B PRO* 3.2 28.0 - - - -
157B GLY* 4.6 6.3 - - - -
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Residues in contact with MET 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A SER* 1.3 71.3 - - - +
20A GLU* 1.3 64.8 + - + +
22A THR* 3.2 5.6 + - - -
23A GLU* 2.9 36.6 + - - +
155A ILE* 5.9 0.4 - - + -
19B MET* 3.5 44.4 - - + +
22B THR* 3.6 30.3 - - + -
23B GLU* 5.2 2.5 - - + -
123B VAL* 4.6 9.2 - - + -
155B ILE* 3.9 20.8 - - + +
156B PRO 3.3 9.0 + - - +
157B GLY* 5.2 3.1 - - - +
158B TYR* 3.9 42.6 - - + +
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Residues in contact with GLU 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A SER* 3.4 6.7 + - - +
19A MET* 1.3 78.1 - - + +
21A GLU* 1.3 53.6 - - + +
23A GLU* 3.1 17.3 + - - +
24A LYS* 2.7 34.8 + - - +
157B GLY 5.9 3.1 - - - +
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Residues in contact with GLU 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A TYR* 2.9 29.8 + - - -
16A PHE 3.9 0.5 - - - +
17A GLN* 3.3 29.6 - - + +
18A SER* 2.7 42.7 + - - +
20A GLU* 1.3 77.8 - - + +
22A THR* 1.3 56.6 + - - +
24A LYS* 3.3 22.2 + - - +
25A TRP* 3.0 35.3 + - - +
52A ASN* 4.6 3.5 + - - +
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Residues in contact with THR 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A GLN* 4.3 4.9 + - - +
18A SER 2.9 22.2 + - - -
19A MET* 3.5 11.3 - - - -
21A GLU* 1.3 70.8 - - - +
23A GLU* 1.3 67.7 + - - +
25A TRP* 3.0 4.8 + - - +
26A MET* 2.9 24.1 + - + +
101A TYR* 3.5 34.5 + - + -
123A VAL* 3.9 23.1 - - + -
19B MET* 3.7 25.6 - - + -
155B ILE* 4.5 9.3 - - + +
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Residues in contact with GLU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A MET* 2.9 20.8 + - - +
20A GLU* 3.1 17.9 + - - +
22A THR* 1.3 75.2 - - - +
24A LYS* 1.3 64.3 + - - +
26A MET* 3.4 3.0 + - - +
27A GLU* 3.1 27.3 + - - +
158A TYR* 3.7 41.1 + - + +
19B MET* 5.1 6.9 - - + +
23B GLU* 5.4 4.2 - - - +
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Residues in contact with LYS 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A GLN* 4.9 0.8 + - - -
20A GLU 2.7 17.0 + - - +
21A GLU* 3.3 24.5 + - - +
23A GLU* 1.3 75.4 - - - +
25A TRP* 1.3 111.8 + - + +
27A GLU* 3.3 20.6 + - - +
28A GLU* 3.3 15.2 + - + +
52A ASN* 5.6 1.4 + - - -
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Residues in contact with TRP 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A GLN* 3.0 31.8 + - - -
21A GLU 3.0 20.5 + - - -
22A THR 3.0 4.4 + - - +
24A LYS* 1.3 114.6 - - + +
26A MET* 1.3 57.7 + - - +
28A GLU* 3.3 19.8 + - - +
29A ALA* 3.0 23.7 + - - +
47A LEU* 3.0 19.9 - - + +
49A VAL* 3.5 21.6 - - + +
52A ASN* 4.8 10.8 - - - -
54A VAL* 3.6 30.7 - - + -
101A TYR* 3.4 48.5 - + + -
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Residues in contact with MET 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A THR* 2.9 19.7 + - + +
23A GLU 3.8 0.4 - - - +
25A TRP* 1.3 75.0 - - - +
27A GLU* 1.3 64.0 + - - +
29A ALA* 3.3 5.5 + - + +
30A MET* 3.0 32.2 + - + +
101A TYR* 3.9 16.6 - - + -
102A VAL 3.5 25.8 - - - +
103A THR* 4.8 3.1 - - - +
123A VAL* 3.7 35.2 - - + +
124A TYR 3.9 4.9 - - - -
125A GLY* 3.9 15.0 - - - +
158A TYR* 3.3 50.0 - - + +
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Residues in contact with GLU 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLU* 3.1 20.5 + - - +
24A LYS* 3.5 15.9 - - - +
26A MET* 1.3 75.4 - - - +
28A GLU* 1.3 63.8 + - - +
30A MET* 3.1 4.7 + - - +
31A HIS* 3.1 34.9 + - + +
158A TYR* 4.6 5.8 + - - +
159A ARG* 3.1 30.9 + - - +
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Residues in contact with GLU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LYS* 3.3 11.9 + - - +
25A TRP* 3.6 20.8 - - - +
26A MET 3.2 0.6 - - - -
27A GLU* 1.3 79.6 - - - +
29A ALA* 1.3 60.6 + - - +
31A HIS* 3.3 13.1 + - + +
32A MET* 3.2 28.4 + - + +
47A LEU* 3.5 22.7 - - + +
54A VAL* 4.9 1.7 - - - +
57A LYS* 3.2 28.1 + - - +
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Residues in contact with ALA 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A TRP 3.0 14.3 + - - +
26A MET* 3.3 13.2 + - + +
28A GLU* 1.3 75.0 - - - +
30A MET* 1.3 56.5 + - - +
32A MET* 3.5 7.0 + - - +
33A ALA 3.0 21.7 + - - -
45A GLY* 3.6 25.2 - - - +
46A CYS* 4.2 2.5 - - - +
47A LEU* 3.6 6.6 - - + +
101A TYR 3.8 19.1 - - - +
102A VAL* 4.8 1.1 - - - -
103A THR* 3.2 16.7 + - - +
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Residues in contact with MET 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A MET* 3.0 22.3 + - + +
27A GLU* 3.2 11.0 - - - +
29A ALA* 1.3 76.2 - - - +
31A HIS* 1.3 64.9 + - - +
33A ALA* 3.3 4.6 + - - +
34A LYS* 3.0 39.7 + - - +
103A THR* 4.1 17.3 - - - +
158A TYR* 5.5 1.6 - - + +
159A ARG* 4.0 30.5 - - + +
162A GLU* 3.5 37.0 - - + +
163A ALA* 4.7 8.3 - - - -
166A MET* 3.3 34.1 - - + +
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Residues in contact with HIS 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A GLU* 3.1 24.6 + - + +
28A GLU* 3.6 13.9 - - + +
30A MET* 1.3 76.6 - - + +
32A MET* 1.3 64.1 + - + +
34A LYS* 3.0 44.3 + - + +
35A GLU* 3.0 19.0 + - - +
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Residues in contact with MET 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A GLU* 3.2 14.7 + - + +
29A ALA* 3.6 9.0 - - - +
31A HIS* 1.3 78.4 - - + +
33A ALA* 1.3 56.3 + - - +
35A GLU* 3.3 18.3 + - - +
36A ALA 2.9 23.4 + - - -
45A GLY* 3.9 8.1 - - - -
46A CYS 4.1 15.7 - - - +
47A LEU* 4.7 8.5 - - - -
57A LYS* 3.8 27.4 - - + -
58A GLY* 3.5 33.4 - - - +
59A ARG* 3.4 41.9 - - + +
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Residues in contact with ALA 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ALA 3.0 14.6 + - - +
30A MET 3.5 9.4 - - - +
32A MET* 1.3 75.1 - - - +
34A LYS* 1.3 60.9 + - - +
36A ALA* 3.1 1.8 + - - +
37A LEU* 3.0 20.1 + - - +
43A PRO* 3.4 33.1 - - - +
44A VAL 4.2 1.1 - - - +
45A GLY* 3.8 10.2 - - - +
103A THR* 3.6 19.3 - - + +
166A MET* 4.3 11.2 - - + -
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Residues in contact with LYS 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A MET* 3.0 34.4 + - - +
31A HIS* 3.0 45.9 + - + +
33A ALA* 1.3 75.7 - - - +
35A GLU* 1.3 62.9 + - + +
37A LEU* 3.2 12.9 + - + +
38A GLU* 3.0 37.8 + - - +
159A ARG* 5.3 5.5 - - - +
166A MET* 4.1 19.6 - - - -
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Residues in contact with GLU 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A HIS* 3.0 13.3 + - - +
32A MET* 3.5 22.6 + - - +
34A LYS* 1.3 75.3 - - + +
36A ALA* 1.3 62.3 + - - +
38A GLU* 3.4 10.8 + - - +
39A ASN* 3.1 33.0 + - - +
59A ARG* 2.8 36.9 + - - +
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Residues in contact with ALA 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A MET 2.9 13.1 + - - +
33A ALA 3.1 8.7 + - - +
35A GLU* 1.3 75.0 - - - +
37A LEU* 1.3 65.6 + - - +
39A ASN* 2.9 14.0 + - - +
41A GLU* 2.9 32.6 + - + +
42A VAL 3.6 21.5 - - - +
43A PRO* 3.8 4.0 - - + -
44A VAL 4.2 5.4 - - - +
59A ARG* 4.2 19.0 - - + +
60A ASN 4.8 0.7 - - - +
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Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ALA 3.0 12.9 + - - +
34A LYS* 3.3 17.3 - - + +
36A ALA* 1.3 75.6 - - - +
38A GLU* 1.3 64.9 + - + +
40A THR* 3.0 21.1 + - - -
41A GLU 3.7 8.3 + - - +
43A PRO* 4.0 11.4 - - + +
166A MET* 3.9 33.4 - - + +
169A THR* 4.1 15.9 - - + -
170A PHE* 3.9 24.3 - - + -
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Residues in contact with GLU 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LYS* 3.0 33.1 + - - +
35A GLU* 3.8 10.3 + - - +
36A ALA 3.2 0.2 - - - -
37A LEU* 1.3 85.1 - - + +
39A ASN* 1.3 63.0 + - - +
40A THR* 3.4 3.9 + - - -
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Residues in contact with ASN 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A GLU* 3.1 22.9 + - - +
36A ALA* 2.9 9.8 + - - +
38A GLU* 1.3 82.0 - - - +
40A THR* 1.3 73.2 + - - +
41A GLU* 3.2 14.1 + - + +
59A ARG* 5.1 8.7 - - - +
63A ASN* 5.0 1.6 + - - +
64A GLN* 4.0 29.5 - - + +
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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
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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