Contacts of the helix formed by residues 5 - 18 (chain A) in PDB entry 1WD5
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 5 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A PHE* 3.3 1.8 - - - +
4A ARG* 1.3 90.3 + - - +
6A ARG* 1.3 64.1 + - - +
7A ARG* 3.2 13.0 + - - +
8A HIS* 2.9 31.1 + - - +
9A ALA 3.2 16.8 + - - -
188A TYR* 3.6 14.4 - - - -
190A ASP* 3.8 29.6 - - + +
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Residues in contact with ARG 6 (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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5A ASP* 1.3 73.6 - - - +
7A ARG* 1.3 61.0 + - - +
9A ALA* 3.5 0.7 + - - +
10A GLY* 3.0 23.9 + - - -
33A GLY* 3.3 29.9 - - - -
36A VAL* 3.7 24.2 - - + -
37A VAL* 3.8 19.2 - - + +
128A ASP* 2.9 22.1 + - + -
188A TYR* 3.8 20.6 - - + -
190A ASP* 4.5 4.0 + - - +
191A PHE* 3.4 37.6 + - - +
192A GLY* 2.9 35.7 + - - +
193A GLU* 5.3 0.2 - - - +
194A VAL* 3.8 15.3 - - - +
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Residues in contact with ARG 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ASP* 3.2 12.1 + - - +
6A ARG* 1.3 74.6 - - - +
8A HIS* 1.3 60.8 + - - +
10A GLY 3.2 0.9 + - - -
11A ALA* 3.0 27.0 + - - +
36A VAL* 3.9 21.2 - - + +
39A ASP* 2.8 34.6 + - - +
40A GLU* 2.9 54.5 + - - +
43A ARG* 4.4 5.0 - - - +
202A ILE* 4.5 17.6 - - - +
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Residues in contact with HIS 8 (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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2A ARG 4.7 4.7 - - - -
3A PHE* 3.7 10.4 - + + -
4A ARG* 3.1 68.1 + - + +
5A ASP* 2.9 25.1 + - - +
7A ARG* 1.3 77.4 - - - +
9A ALA* 1.3 61.7 + - - +
11A ALA* 3.3 5.3 + - - +
12A LEU* 3.2 43.0 + - + +
2955A MES 4.3 14.9 - - - -
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Residues in contact with ALA 9 (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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3A PHE* 3.8 30.0 - - + -
5A ASP 3.2 2.4 + - - -
6A ARG* 3.8 6.7 - - - +
8A HIS* 1.3 79.6 - - - +
10A GLY* 1.3 58.5 + - - +
12A LEU* 3.4 3.0 + - - +
13A LEU* 2.9 30.2 + - - +
37A VAL* 4.5 2.2 - - + -
156A PRO* 3.7 14.5 - - + +
175A LEU* 4.0 2.9 - - - +
188A TYR* 3.6 28.3 - - + +
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Residues in contact with GLY 10 (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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6A ARG 3.0 13.4 + - - -
7A ARG 3.2 4.0 + - - -
8A HIS 3.2 0.2 - - - -
9A ALA* 1.3 77.9 - - - +
11A ALA* 1.3 55.7 + - - +
13A LEU* 3.4 1.7 + - - -
14A ALA* 3.0 28.9 + - - +
37A VAL* 3.7 29.6 - - - +
40A GLU* 3.8 9.4 - - - -
41A VAL* 3.5 7.3 - - - +
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Residues in contact with ALA 11 (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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7A ARG 3.0 12.7 + - - +
8A HIS* 3.6 10.1 - - - +
9A ALA 3.3 0.2 - - - -
10A GLY* 1.3 76.4 - - - +
12A LEU* 1.3 62.6 + - - +
14A ALA* 3.3 4.3 + - - +
15A GLU* 3.1 29.1 + - - +
40A GLU* 3.7 0.6 - - - +
44A ARG* 3.7 40.4 - - - +
2955A MES 3.8 20.0 - - - +
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Residues in contact with LEU 12 (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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1A MSE 4.8 8.3 - - + -
3A PHE* 3.9 26.2 - - + -
8A HIS* 3.2 29.4 + - + +
9A ALA 3.8 2.7 - - - +
11A ALA* 1.3 80.1 - - - +
13A LEU* 1.3 62.1 + - - +
15A GLU* 3.3 11.8 + - - +
16A ALA* 3.1 21.8 + - - +
175A LEU* 3.7 17.5 - - + +
2955A MES 3.5 31.9 - - - -
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Residues in contact with LEU 13 (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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9A ALA 2.9 17.5 + - - +
10A GLY 3.7 4.9 - - - +
11A ALA 3.2 0.2 - - - -
12A LEU* 1.3 76.6 - - - +
14A ALA* 1.3 64.5 + - - +
16A ALA* 3.1 3.8 + - - +
17A LEU* 3.0 31.4 + - + +
37A VAL* 4.1 10.5 - - + -
41A VAL* 4.2 7.2 - - + -
126A VAL* 3.9 17.9 - - + -
154A ALA* 3.6 37.5 - - + +
155A VAL 3.9 20.4 - - - +
156A PRO* 4.1 6.1 - - + -
173A VAL* 4.1 10.3 - - + +
175A LEU* 3.8 27.3 - - + +
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Residues in contact with ALA 14 (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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10A GLY 3.0 16.6 + - - +
11A ALA 3.3 5.1 + - - +
13A LEU* 1.3 76.2 - - - +
15A GLU* 1.3 59.2 + - + +
17A LEU* 3.2 11.9 + - - +
18A ALA* 3.0 25.3 + - - +
41A VAL* 4.1 14.5 - - - +
44A ARG* 3.5 33.4 - - + -
45A LEU* 3.7 13.4 - - + +
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Residues in contact with GLU 15 (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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11A ALA 3.1 18.2 + - - +
12A LEU* 3.5 17.2 - - + +
14A ALA* 1.3 76.1 - - + +
16A ALA* 1.3 64.6 + - - +
18A ALA* 3.5 7.7 + - - +
19A PRO* 3.3 18.9 - - - +
44A ARG* 4.5 7.7 + - - -
2955A MES 2.7 72.3 + - + +
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Residues in contact with ALA 16 (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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12A LEU 3.1 6.6 + - - +
13A LEU 3.1 8.0 + - - +
15A GLU* 1.3 76.9 - - - +
17A LEU* 1.3 57.7 + - - +
18A ALA 3.5 0.2 - - - -
19A PRO* 3.4 13.1 - - - +
20A LEU* 4.5 6.9 - - - +
173A VAL* 4.0 19.0 - - + +
175A LEU* 3.7 28.7 - - + -
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Residues in contact with LEU 17 (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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13A LEU* 3.0 22.9 + - + +
14A ALA 3.7 4.0 - - - +
15A GLU 3.2 0.2 - - - -
16A ALA* 1.3 76.8 - - - +
18A ALA* 1.3 65.4 + - - +
19A PRO* 3.3 3.1 - - - -
20A LEU* 3.0 43.6 + - + +
21A GLY 4.4 0.5 + - - -
22A LEU* 4.5 12.2 + - + +
41A VAL* 3.9 27.6 - - + -
45A LEU* 4.1 15.6 - - + +
124A VAL* 4.1 10.5 - - + -
152A VAL* 4.1 7.6 - - + -
154A ALA* 3.9 27.8 - - + -
173A VAL* 3.8 20.2 - - + -
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Residues in contact with ALA 18 (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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14A ALA 3.0 13.3 + - - +
15A GLU* 3.7 11.2 - - - +
17A LEU* 1.3 76.2 - - - +
19A PRO* 1.3 67.5 - - + +
20A LEU 3.3 0.9 + - - -
21A GLY* 3.6 9.4 + - - -
22A LEU 5.1 0.5 + - - -
45A LEU* 4.1 13.9 - - + -
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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