Contacts of the helix formed by residues 4 - 20 (chain H) in PDB entry 3DUF
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 THR 4 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3H MET* 1.3 78.5 - - - +
5H MET* 1.3 65.5 + - - +
6H VAL* 3.3 21.0 - - - +
7H GLN* 3.0 23.8 + - - +
8H ALA* 3.1 17.2 + - - +
150H PRO* 3.7 2.0 - - - -
176H TYR 3.5 11.0 - - - -
177H ARG* 3.9 20.6 - - + +
179H PHE 3.5 20.4 - - - +
180H ARG* 4.8 5.4 - - + -
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Residues in contact with MET 5 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H THR* 1.3 73.2 - - - +
6H VAL* 1.3 63.7 + - - +
8H ALA* 3.1 4.2 + - - +
9H ILE* 3.0 25.2 + - + +
147H PRO* 4.5 17.9 - - - +
148H SER 4.6 11.9 - - - -
149H THR 4.7 0.2 - - - -
150H PRO* 3.5 22.2 - - + +
153H ALA* 3.8 25.8 - - + -
171H GLU* 4.2 10.8 - - + -
172H HIS* 3.6 38.4 - - + +
175H LEU* 3.3 36.5 + - + +
176H TYR* 3.2 17.1 + - + +
179H PHE* 4.5 1.6 + - + -
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Residues in contact with VAL 6 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H THR* 3.3 14.6 - - - +
5H MET* 1.3 76.5 - - - +
7H GLN* 1.3 69.7 + - + +
9H ILE* 3.2 12.7 + - + +
10H THR* 3.1 26.6 + - - +
37H PHE* 3.5 25.4 - - + +
38H ARG* 4.4 4.3 - - + +
39H ALA* 4.0 20.4 - - + +
176H TYR* 3.0 35.2 + - + +
177H ARG* 4.8 6.1 - - + -
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Residues in contact with GLN 7 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2H GLN 4.3 4.0 + - - +
3H MET* 3.5 21.3 - - + +
4H THR* 3.0 40.0 + - - +
6H VAL* 1.3 84.5 - - + +
8H ALA* 1.3 65.2 + - - +
10H THR* 3.5 8.5 + - - -
11H ASP* 3.1 23.6 + - - +
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Residues in contact with ALA 8 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3H MET* 3.9 17.2 - - - -
4H THR 3.1 10.9 + - - +
5H MET 3.1 9.7 + - - +
7H GLN* 1.3 78.2 - - - +
9H ILE* 1.3 58.8 + - - +
11H ASP* 3.4 3.1 + - - +
12H ALA* 3.0 28.6 + - - +
150H PRO* 3.3 34.5 - - + +
153H ALA* 4.5 1.1 - - + -
154H LYS* 3.8 17.4 - - + +
183H VAL* 5.1 0.2 - - + -
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Residues in contact with ILE 9 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H MET* 3.0 28.3 + - + +
6H VAL* 3.2 10.1 + - + +
8H ALA* 1.3 74.3 - - - +
10H THR* 1.3 65.9 + - - +
12H ALA* 3.1 3.7 + - - +
13H LEU* 3.0 31.5 + - + +
39H ALA* 4.9 6.5 - - + -
115H ARG* 3.9 14.1 - - - +
153H ALA* 4.4 13.9 - - + -
157H LEU* 3.9 21.1 - - + -
169H PHE* 4.7 3.6 - - + -
171H GLU* 3.2 40.8 - - + +
176H TYR* 3.9 19.3 - - + -
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Residues in contact with THR 10 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H VAL* 3.1 16.3 + - - +
7H GLN* 3.8 10.0 - - - -
8H ALA 3.4 0.2 - - - -
9H ILE* 1.3 75.9 - - - +
11H ASP* 1.3 62.4 + - - +
13H LEU* 3.4 6.0 + - - +
14H ARG* 3.1 43.9 + - - +
38H ARG 4.0 5.7 + - - +
39H ALA* 2.8 28.5 + - - +
41H GLU* 4.3 17.0 - - + +
43H LEU* 4.5 9.3 - - + +
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Residues in contact with ASP 11 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3H MET* 4.4 12.8 - - - +
7H GLN 3.1 17.1 + - - +
8H ALA* 3.6 7.6 - - - +
9H ILE 3.2 0.2 - - - -
10H THR* 1.3 78.5 - - - +
12H ALA* 1.3 61.6 + - - +
14H ARG* 3.4 17.9 + - - +
15H ILE* 3.1 35.8 + - - +
154H LYS* 2.5 39.1 + - + +
185H GLU* 5.2 0.7 - - - -
186H GLY 5.0 0.5 + - - -
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Residues in contact with ALA 12 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H ALA 3.0 13.9 + - - +
9H ILE 3.1 8.3 + - - +
11H ASP* 1.3 77.1 - - - +
13H LEU* 1.3 62.8 + - - +
15H ILE* 3.2 5.9 + - - +
16H GLU* 3.2 25.9 + - - +
154H LYS* 3.9 20.8 - - + +
157H LEU* 3.6 30.5 - - + -
158H ILE* 4.2 13.2 - - + +
161H ILE* 6.5 0.2 - - - -
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Residues in contact with LEU 13 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H ILE* 3.0 34.3 + - + +
10H THR* 3.8 4.3 - - - +
12H ALA* 1.3 75.2 - - - +
14H ARG* 1.3 58.2 + - - +
16H GLU* 3.3 5.0 + - + +
17H LEU* 3.0 35.3 + - - +
23H VAL* 5.6 0.7 - - + +
25H ILE* 4.2 12.1 - - + -
39H ALA 4.3 5.6 - - - +
40H THR* 4.2 25.4 - - + -
43H LEU* 3.9 15.3 - - + -
77H VAL* 4.3 15.7 - - + -
115H ARG* 4.2 21.5 - - - +
157H LEU* 3.9 20.6 - - + -
161H ILE* 5.2 5.8 - - + -
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Residues in contact with ARG 14 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H THR* 3.1 39.3 + - - +
11H ASP* 3.7 16.3 + - - +
12H ALA 3.3 0.4 - - - -
13H LEU* 1.3 72.6 - - - +
15H ILE* 1.3 66.9 + - + +
17H LEU* 3.5 4.6 + - - +
18H LYS* 3.2 22.7 + - + +
41H GLU 5.0 4.0 + - - -
42H GLY* 4.6 6.1 + - - -
43H LEU* 3.5 24.1 - - + +
46H GLU* 2.7 48.2 + - - +
47H PHE* 4.1 3.8 - - + -
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Residues in contact with ILE 15 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H ASP* 3.1 25.5 + - - +
12H ALA 3.2 7.1 + - - +
14H ARG* 1.3 79.4 - - + +
16H GLU* 1.3 67.5 + - - +
18H LYS* 3.4 5.5 + - - +
19H ASN* 3.0 32.7 + - - +
154H LYS* 3.7 16.8 - - - +
158H ILE* 4.4 8.1 - - + -
186H GLY* 3.5 33.4 - - - +
187H GLU* 3.9 23.8 - - + +
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Residues in contact with GLU 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H ALA 3.2 14.5 + - - +
13H LEU* 3.9 5.4 - - - +
15H ILE* 1.3 80.3 - - - +
17H LEU* 1.3 65.7 + - - +
18H LYS 3.1 0.2 - - - -
19H ASN* 4.0 9.7 - - - +
20H ASP* 3.0 29.8 + - - +
23H VAL* 3.7 15.6 - - + +
75H ARG* 5.3 1.6 - - - -
158H ILE* 3.8 20.0 - - + +
161H ILE* 3.9 37.2 - - + +
162H ARG* 3.4 49.5 + - - +
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Residues in contact with LEU 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H LEU 3.0 22.7 + - - +
14H ARG 3.9 0.7 - - - +
15H ILE 3.3 0.2 - - - -
16H GLU* 1.3 77.3 - - - +
18H LYS* 1.3 60.9 + - - +
20H ASP 3.7 3.7 - - - +
21H PRO* 4.7 0.7 - - - +
23H VAL* 3.8 32.5 - - + +
25H ILE* 3.6 30.5 - - + -
43H LEU* 4.0 18.8 - - + -
47H PHE* 3.8 40.4 - - + -
51H ARG* 3.3 48.3 + - + +
52H VAL* 4.6 4.0 - - + -
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Residues in contact with LYS 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H ARG* 3.2 17.4 + - + +
15H ILE* 3.8 5.4 - - - +
16H GLU 3.1 0.4 - - - -
17H LEU* 1.3 79.7 - - - +
19H ASN* 1.3 66.3 + - - +
20H ASP 5.2 0.2 - - - -
21H PRO* 5.4 1.4 - - - +
46H GLU* 5.8 1.3 - - - +
47H PHE* 4.1 18.6 - - + -
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Residues in contact with ASN 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H ILE* 3.0 24.8 + - - +
16H GLU* 3.3 14.3 + - - +
18H LYS* 1.3 85.5 + - - +
20H ASP* 1.3 59.5 + - + +
21H PRO* 3.8 6.9 - - - +
162H ARG* 3.2 25.2 + - - +
187H GLU* 4.8 6.1 - - - +
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Residues in contact with ASP 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H GLU* 3.0 18.3 + - - +
17H LEU 4.2 2.2 - - - -
19H ASN* 1.3 80.7 - - + +
21H PRO* 1.3 67.0 - - - +
22H ASN* 2.8 40.8 + - - +
23H VAL* 3.1 20.1 + - + -
51H ARG* 3.1 13.1 + - - -
75H ARG* 3.3 27.6 + - - -
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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