Contacts of the helix formed by residues 13 - 27 (chain A) in PDB entry 2W5U
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 GLY 13 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A THR* 2.5 27.2 + - - +
12A SER* 1.3 74.1 - - - +
14A ASN* 1.3 64.1 + - - +
15A ALA 3.4 1.1 - - - -
16A GLU* 3.6 22.7 - - - +
17A ALA* 3.0 25.1 + - - +
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Residues in contact with ASN 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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12A SER* 3.3 6.9 + - - -
13A GLY* 1.3 78.4 - - - +
15A ALA* 1.3 59.0 + - - +
17A ALA* 3.2 4.8 + - - +
18A ILE* 2.9 34.1 + - - +
86A LEU* 4.1 8.3 - - + -
141A GLU* 4.0 28.6 + - + +
142A ASP* 5.0 1.9 - - - +
165A FMN 2.9 53.4 + - - +
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Residues in contact with ALA 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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8A PHE* 4.2 6.3 - - + -
9A GLY 3.3 26.0 - - - +
10A THR* 4.0 1.3 - - - -
14A ASN* 1.3 71.3 - - - +
16A GLU* 1.3 52.3 + - - +
18A ILE* 3.1 4.2 + - - +
19A ALA* 2.7 35.9 + - - +
51A VAL* 3.7 21.3 - - + +
53A PRO* 3.8 13.0 - - + -
86A LEU* 4.1 10.0 - - + +
165A FMN 2.7 17.0 + - - +
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Residues in contact with GLU 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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8A PHE* 3.5 41.8 - - + -
10A THR* 4.0 10.6 - - + +
13A GLY* 3.6 20.9 + - - +
14A ASN 3.3 0.4 - - - -
15A ALA* 1.3 76.1 - - - +
17A ALA* 1.3 61.2 + - - +
19A ALA* 3.4 1.7 + - - +
20A GLU* 3.0 29.5 + - + +
31A VAL* 5.2 1.7 - - + +
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Residues in contact with ALA 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 GLY 3.0 19.2 + - - +
14A ASN* 3.5 5.6 - - - +
16A GLU* 1.3 76.9 - - - +
18A ILE* 1.3 60.4 + - + +
20A GLU* 3.2 8.3 + - - +
21A LYS* 2.9 39.9 + - - +
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Residues in contact with ILE 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 ASN 2.9 16.6 + - - +
15A ALA* 3.3 10.1 - - - +
17A ALA* 1.3 78.6 - - + +
19A ALA* 1.3 56.9 + - - +
21A LYS* 3.3 6.7 + - + +
22A ILE* 2.8 56.8 + - + +
51A VAL* 3.9 13.9 - - + -
84A VAL* 4.3 8.7 - - + -
86A LEU* 3.6 20.2 - - + -
139A ILE* 4.0 14.4 - - + -
141A GLU* 4.2 7.9 - - + +
148A THR* 3.2 35.9 - - + -
152A ILE* 4.0 7.0 - - + -
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Residues in contact with ALA 19 (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 ILE* 3.8 19.4 - - + +
8A PHE* 3.8 20.4 - - + -
15A ALA 2.7 18.6 + - - +
16A GLU 3.8 2.0 - - - +
18A ILE* 1.3 71.3 - - - +
20A GLU* 1.3 61.2 + - - +
22A ILE* 3.7 5.7 - - - +
23A SER* 2.9 29.1 + - - -
31A VAL* 3.9 7.9 - - + +
51A VAL* 3.6 23.3 - - + -
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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
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16A GLU* 3.0 15.3 + - + +
17A ALA* 3.3 13.0 - - - +
18A ILE 3.2 0.2 - - - -
19A ALA* 1.3 73.3 - - - +
21A LYS* 1.3 55.3 - - + +
23A SER* 3.0 9.0 + - - -
24A LYS* 2.7 69.3 + - + +
31A VAL* 4.0 18.8 - - + +
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Residues in contact with LYS 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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17A ALA* 2.9 23.7 + - - +
18A ILE* 3.4 11.6 - - + +
20A GLU* 1.3 76.0 - - + +
22A ILE* 1.3 58.1 + - - +
24A LYS* 2.9 27.3 + - - +
25A ALA* 2.9 16.5 + - - +
141A GLU* 5.4 1.4 + - - -
145A ASP* 5.9 1.2 + - - -
148A THR* 4.2 15.1 - - + +
149A ASP* 2.9 36.5 + - - +
152A ILE* 3.7 23.8 - - + -
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Residues in contact with ILE 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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6A ILE* 4.2 7.4 - - + -
18A ILE* 2.8 51.4 + - + +
19A ALA* 3.8 8.1 - - - +
20A GLU 3.3 0.2 - - - -
21A LYS* 1.3 72.4 - - - +
23A SER* 1.3 56.4 + - - +
25A ALA* 4.0 0.6 - - - +
26A ILE* 3.1 27.8 + - + +
49A ILE* 4.2 28.9 - - + -
51A VAL* 5.1 2.5 - - + -
84A VAL* 3.7 28.5 - - + -
137A LEU* 4.6 5.8 - - + -
152A ILE* 4.1 25.1 - - + -
155A TRP* 4.3 10.3 - - + -
156A VAL* 4.5 8.5 - - + -
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Residues in contact with SER 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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6A ILE* 3.5 9.9 - - - +
19A ALA 2.9 14.8 + - - -
20A GLU* 3.3 11.0 - - - -
22A ILE* 1.3 77.5 - - - +
24A LYS* 1.3 66.8 + - - +
25A ALA 3.2 0.2 - - - -
26A ILE* 4.3 2.5 - - - -
27A GLY* 3.0 24.6 + - - -
29A ALA* 2.9 33.3 + - - +
31A VAL* 3.7 16.4 - - - +
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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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20A GLU* 2.7 46.1 + - + +
21A LYS* 3.1 13.7 - - + +
23A SER* 1.3 78.4 - - - +
25A ALA* 1.3 60.3 + - + +
27A GLY* 4.2 3.6 + - - -
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Residues in contact with ALA 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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21A LYS 2.9 13.3 + - - +
22A ILE 4.3 0.7 - - - +
24A LYS* 1.3 78.2 - - + +
26A ILE* 1.3 64.7 + - - +
27A GLY* 3.3 0.7 - - - -
152A ILE* 4.3 11.2 - - + +
153A SER* 5.5 4.3 - - - -
156A VAL* 3.9 27.5 - - + +
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Residues in contact with ILE 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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4A ILE* 3.9 23.5 - - + +
6A ILE* 4.6 5.8 - - + -
22A ILE* 3.1 25.1 + - + +
23A SER* 4.3 4.9 - - - -
25A ALA* 1.3 79.0 - - - +
27A GLY* 1.3 75.2 + - - +
28A ASN* 5.2 0.2 - - - +
29A ALA* 4.4 6.3 - - + -
49A ILE* 4.7 10.3 - - + -
156A VAL* 3.3 33.5 - - + +
159A VAL* 3.5 31.0 - - + -
160A ARG* 4.0 11.4 - - + +
163A PHE* 4.6 5.4 - - + +
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Residues in contact with GLY 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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4A ILE* 3.4 14.0 - - - +
23A SER 3.0 21.2 + - - -
24A LYS 4.5 3.1 - - - -
25A ALA 3.3 2.9 - - - -
26A ILE* 1.3 85.6 - - - +
28A ASN* 1.3 72.6 + - - +
29A ALA* 3.3 2.9 + - - -
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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