Contacts of the helix formed by residues 14 - 28 (chain A) in PDB entry 3K9W
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 14 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A PRO* 3.6 15.9 - - + +
13A LEU* 1.3 76.4 - - - +
15A ARG* 1.3 64.0 + - - +
16A GLY* 3.1 13.8 + - - -
17A HIS* 2.9 30.9 + - + +
18A GLU* 3.0 22.7 + - - +
126A ILE* 4.2 20.3 - - + +
128A GLY* 4.5 17.3 - - - +
131A VAL* 4.7 2.5 - - + -
144A PHE 3.5 11.7 - - - -
145A VAL* 4.1 14.6 - - + -
146A PHE* 5.2 3.4 - - - -
168A ADE 4.5 5.6 + - - +
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Residues in contact with ARG 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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14A THR* 1.3 69.2 - - - +
16A GLY* 1.3 64.7 + - - +
18A GLU* 3.9 3.0 - - - +
19A ASP* 3.1 23.7 + - - +
123A TYR* 3.8 37.1 + - + -
126A ILE* 4.4 1.1 - - + -
142A SER* 3.0 29.6 + - - +
143A LYS* 3.5 18.9 + - - +
144A PHE 2.9 20.6 + - - +
145A VAL* 3.2 22.3 + - - +
146A PHE* 3.6 46.7 - - + +
147A PRO* 4.0 11.5 - - - +
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Residues in contact with GLY 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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14A THR* 3.1 7.7 + - - -
15A ARG* 1.3 78.0 - - - +
17A HIS* 1.3 61.9 + - - +
19A ASP* 3.3 4.2 + - - +
20A LEU* 3.1 17.0 + - - +
119A PRO* 4.2 1.8 - - - +
123A TYR* 3.7 16.7 - - - +
126A ILE* 4.3 2.8 - - - +
168A ADE 3.3 39.2 - - - -
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Residues in contact with HIS 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A TYR* 3.3 25.0 - - + +
10A PHE* 3.5 24.0 - + + -
11A ASP 5.3 0.2 - - - -
12A PRO 3.8 15.0 - - - -
13A LEU* 3.5 23.1 - - + -
14A THR* 2.9 35.6 + - + +
16A GLY* 1.3 77.0 - - - +
18A GLU* 1.3 58.0 + - - +
20A LEU* 3.1 3.8 + - - +
21A VAL* 2.9 32.5 + - - +
128A GLY* 6.1 2.2 - - - -
167A 4PS 3.3 27.7 + - - -
168A ADE 3.9 22.4 + + - -
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Residues in contact with GLU 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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13A LEU* 4.6 3.3 - - + +
14A THR 3.0 13.0 + - - +
15A ARG 3.9 3.8 - - - +
16A GLY 3.3 0.2 - - - -
17A HIS* 1.3 75.9 - - - +
19A ASP* 1.3 64.4 + - - +
21A VAL* 3.2 6.7 + - - +
22A ARG* 2.9 29.5 + - - +
57A VAL* 3.7 19.9 - - + +
58A LEU* 3.9 13.5 - - + -
60A HIS* 4.6 3.5 + - - -
61A TYR* 2.6 28.8 + - - -
123A TYR* 5.9 0.9 - - - -
146A PHE* 3.6 40.7 - - + -
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Residues in contact with ASP 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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15A ARG 3.1 19.0 + - - +
16A GLY 3.7 4.9 - - - +
17A HIS 3.2 0.2 - - - -
18A GLU* 1.3 82.3 + - - +
20A LEU* 1.3 56.6 + - - +
22A ARG* 2.8 34.0 + - - +
23A ARG* 2.8 47.8 + - - +
119A PRO* 3.3 5.1 - - + +
120A SER* 2.8 37.8 + - - -
123A TYR* 3.7 19.2 - - + -
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Residues in contact with LEU 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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6A TYR* 3.6 27.4 - - + +
16A GLY 3.1 9.5 + - - +
17A HIS 3.1 8.0 + - - +
19A ASP* 1.3 76.7 - - - +
21A VAL* 1.3 56.5 + - - +
23A ARG* 3.4 4.3 + - - +
24A ALA* 2.8 33.7 + - + +
86A VAL* 3.5 31.0 - - + -
88A GLY* 4.0 12.6 - - - -
117A MET* 3.8 31.9 - - + +
118A THR 3.9 3.8 - - - +
119A PRO* 3.7 34.8 - - + -
168A ADE 4.5 2.5 - - + -
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Residues in contact with VAL 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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6A TYR* 3.6 24.9 - - + -
13A LEU* 5.3 1.6 - - + -
17A HIS 2.9 19.5 + - - +
18A GLU 3.6 7.0 - - - +
20A LEU* 1.3 74.3 - - - +
22A ARG* 1.3 64.4 + - - +
25A SER* 2.9 26.9 + - - -
31A LEU* 3.8 10.9 - - + +
33A VAL* 3.9 13.0 - - + -
58A LEU* 3.9 28.5 - - + -
61A TYR* 4.3 6.7 - - + -
64A VAL* 3.7 31.9 - - + -
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Residues in contact with ARG 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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18A GLU* 2.9 15.5 + - - +
19A ASP* 2.8 33.2 + - - +
21A VAL* 1.3 75.8 - - - +
23A ARG* 1.3 99.8 + - - +
25A SER* 3.2 17.1 + - - -
26A SER* 3.4 12.8 + - - -
61A TYR* 3.3 34.3 + - + +
120A SER* 4.1 1.4 + - - -
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Residues in contact with ARG 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 ASP* 2.8 35.7 + - - +
20A LEU* 3.8 6.7 - - + +
22A ARG* 1.3 101.3 - - - +
24A ALA* 1.3 60.8 + - - +
26A SER* 2.7 25.6 + - - -
27A ILE* 3.6 8.7 + - - +
117A MET* 3.9 17.2 - - + +
118A THR 3.5 23.8 + - - +
119A PRO* 4.5 1.3 - - - -
120A SER* 2.7 33.4 + - - +
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Residues in contact with ALA 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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6A TYR* 5.9 0.4 - - + -
20A LEU* 2.8 21.9 + - + +
23A ARG* 1.3 73.3 - - - +
25A SER* 1.3 58.6 + - - +
27A ILE* 3.1 2.4 + - - -
28A PHE* 3.1 34.0 + - + +
31A LEU* 3.8 26.9 - - + -
86A VAL* 4.2 13.7 - - + -
117A MET* 3.7 24.4 - - - +
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Residues in contact with SER 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 VAL 2.9 23.4 + - - -
22A ARG* 3.2 11.3 + - - -
24A ALA* 1.3 76.6 - - - +
26A SER* 1.3 59.3 + - - +
27A ILE 3.3 0.4 - - - -
28A PHE 3.3 5.3 - - - +
31A LEU* 4.1 9.8 - - - +
61A TYR* 4.2 10.0 - - - -
63A ASN* 2.8 45.0 + - - +
64A VAL* 3.7 21.2 - - - +
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Residues in contact with SER 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 ARG 3.4 11.2 + - - -
23A ARG* 2.7 21.4 + - - -
24A ALA 3.1 0.8 - - - -
25A SER* 1.3 76.2 - - - +
27A ILE* 1.3 72.3 + - - +
28A PHE 4.8 0.2 - - - -
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Residues in contact with ILE 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 ARG 3.7 13.5 - - - +
24A ALA* 3.1 6.6 + - - +
26A SER* 1.3 92.2 - - - +
28A PHE* 1.3 87.4 + - + +
29A ASP* 4.1 2.4 + - - +
117A MET* 4.3 14.8 - - + -
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Residues in contact with PHE 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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2A VAL* 3.7 25.8 - - + +
4A ALA* 3.6 15.9 - - + -
24A ALA* 3.1 29.4 + - + +
25A SER* 3.3 5.5 - - - +
26A SER 4.8 0.2 - - - -
27A ILE* 1.3 99.2 - - + +
29A ASP* 1.3 66.7 + - - +
30A THR* 3.3 18.1 - - - +
31A LEU* 4.8 1.6 - - + +
63A ASN* 3.1 17.0 + - - -
84A VAL* 3.8 34.8 - - + -
86A VAL* 3.6 22.4 - - + -
115A MET* 4.2 14.8 - - + -
117A MET* 4.9 5.8 - - - -
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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