Contacts of the helix formed by residues 13 - 29 (chain A) in PDB entry 3KAP
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 SER* 3.2 15.3 + - - -
11A SER 3.5 2.0 - - - -
12A THR* 1.3 78.5 - - - +
14A ASN* 1.3 58.5 + - - +
16A GLU* 3.5 18.1 - - - +
17A SER* 3.0 28.2 + - - -
129A ASP* 5.1 0.7 - - - +
150A FMN 3.1 1.2 + - - -
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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 THR* 3.6 18.4 + - - +
13A GLY* 1.3 77.3 - - - +
15A THR* 1.3 61.6 + - - +
17A SER* 2.8 24.1 + - - -
18A ILE* 3.3 10.2 - - - +
93A SER* 3.2 21.9 + - - +
128A GLY* 3.4 19.4 - - - +
129A ASP* 3.5 16.4 + - - +
150A FMN 3.0 33.3 + - - +
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Residues in contact with THR 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* 4.4 3.1 - - + -
9A GLY 3.8 11.9 - - - +
10A SER* 4.4 0.2 - - - -
14A ASN* 1.3 68.8 - - - +
16A GLU* 1.3 60.3 + - - +
18A ILE* 3.3 10.2 + - - +
19A ALA* 2.9 27.1 + - - +
56A GLY 3.7 24.9 - - - +
57A CYS* 3.8 4.5 - - - +
58A SER* 3.7 9.9 + - - -
91A PHE* 3.7 25.7 - - + -
92A ALA* 4.5 0.4 - - - -
93A SER* 3.4 21.8 + - - +
150A FMN 2.7 23.0 + - - -
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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 40.0 - - + -
10A SER* 3.2 18.7 + - - +
13A GLY* 3.5 20.2 + - - +
14A ASN 3.2 0.2 - - - -
15A THR* 1.3 76.5 - - - +
17A SER* 1.4 56.5 + - - +
19A ALA* 3.1 4.2 + - - +
20A GLN* 3.0 30.5 + - + +
35A LEU* 5.9 1.5 - - + +
37A ASN* 5.0 5.7 + - - -
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Residues in contact with SER 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 14.1 + - - -
14A ASN 2.8 18.3 + - - -
16A GLU* 1.4 72.0 - - - +
18A ILE* 1.3 58.8 + - - +
20A GLN* 3.5 8.5 + - - +
21A LYS* 3.0 28.4 + - - +
129A ASP* 3.3 15.9 - - - +
130A ALA* 2.9 32.7 + - - +
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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 3.3 15.9 - - - +
15A THR* 3.5 9.9 - - + +
16A GLU 3.2 0.4 - - - -
17A SER* 1.3 76.3 - - - +
19A ALA* 1.3 57.4 + - - +
21A LYS* 3.1 3.9 + - - +
22A LEU* 2.9 33.7 + - + +
91A PHE* 3.7 17.0 - - + -
92A ALA* 3.8 25.6 - - - +
93A SER* 3.8 18.2 - - - +
124A LEU* 3.7 27.1 - - + -
126A ILE* 3.9 16.8 - - + -
128A GLY 4.6 0.2 - - - +
130A ALA* 4.0 22.0 - - + +
137A VAL* 4.8 6.7 - - + -
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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 20.9 - - + +
8A PHE* 3.6 34.8 - - + -
15A THR 2.9 13.4 + - - +
16A GLU 3.1 9.2 + - - +
18A ILE* 1.3 76.7 - - - +
20A GLN* 1.3 56.4 + - - +
22A LEU* 3.4 5.1 + - - +
23A GLU* 2.9 28.9 + - - +
35A LEU* 3.8 5.4 - - + -
91A PHE* 4.0 9.6 - - + -
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Residues in contact with GLN 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 17.0 + - + +
17A SER* 3.7 8.7 - - - +
18A ILE 3.2 0.2 - - - -
19A ALA* 1.3 74.4 - - - +
21A LYS* 1.3 65.8 + - - +
23A GLU* 3.2 20.0 + - - +
24A GLU* 3.1 22.2 + - - +
35A LEU* 3.7 25.7 - - + +
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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 SER 3.0 17.7 + - - +
18A ILE 3.1 3.6 + - - +
20A GLN* 1.3 76.1 - - - +
22A LEU* 1.3 62.8 + - - +
24A GLU* 3.1 37.5 + - - +
25A LEU* 3.0 51.8 + - + +
130A ALA* 4.2 12.1 - - + -
134A PRO* 6.5 1.3 - - + -
137A VAL* 3.7 25.8 - - + -
138A SER* 5.4 3.8 - - - +
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Residues in contact with LEU 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* 3.9 9.9 - - + -
18A ILE* 2.9 24.0 + - + +
19A ALA 3.6 5.2 - - - +
21A LYS* 1.3 75.6 - - - +
23A GLU* 1.3 65.8 + - - +
25A LEU* 3.3 2.0 + - + +
26A VAL* 2.8 32.0 + - + +
54A LEU* 4.3 13.9 - - + -
91A PHE* 4.0 31.2 - - + -
124A LEU* 5.1 0.2 - - + -
137A VAL* 3.8 25.6 - - + +
140A PHE* 4.0 33.9 - - + -
141A ALA* 4.1 18.8 - - + -
144A VAL* 6.1 0.2 - - + -
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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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6A ILE* 3.6 15.1 - - + +
19A ALA 2.9 14.2 + - - +
20A GLN* 3.2 23.9 + - - +
22A LEU* 1.3 75.7 - - - +
24A GLU* 1.3 81.6 + - - +
26A VAL* 4.2 0.2 - - - +
27A ALA* 2.9 41.2 + - - +
33A VAL* 4.0 22.8 - - + +
35A LEU* 4.2 25.8 - - + +
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Residues in contact with GLU 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 GLN* 3.1 13.8 + - - +
21A LYS* 3.1 41.9 + - - +
22A LEU 3.3 0.2 - - - -
23A GLU* 1.3 91.2 + - - +
25A LEU* 1.3 62.8 + - + +
27A ALA* 3.8 3.2 - - - +
28A ALA* 3.0 30.8 + - + +
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Residues in contact with LEU 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* 3.0 48.7 + - + +
22A LEU* 4.1 1.8 - - + +
24A GLU* 1.3 81.6 - - + +
26A VAL* 1.3 64.0 + - - +
28A ALA* 3.5 8.6 + - + +
29A GLY 3.2 16.3 + - - -
137A VAL* 4.6 2.2 - - + +
138A SER* 4.1 25.6 - - - +
141A ALA* 3.8 29.2 - - + -
145A LEU* 3.7 12.9 - - + +
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Residues in contact with VAL 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 VAL* 3.9 25.4 - - + -
6A ILE* 5.0 0.9 - - + -
22A LEU* 2.8 27.3 + - + +
25A LEU* 1.3 71.5 - - - +
27A ALA* 1.3 65.8 + - - +
29A GLY* 3.3 5.0 + - - -
31A HIS* 3.3 26.9 + - + -
33A VAL* 3.8 20.9 - - + -
54A LEU* 4.4 12.8 - - + -
141A ALA* 5.1 5.8 - - + -
144A VAL* 3.8 27.1 - - + -
145A LEU* 3.9 7.2 - - + -
148A LEU* 4.1 9.4 - - + -
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Residues in contact with ALA 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* 2.9 32.8 + - - +
24A GLU* 3.8 4.0 - - - +
26A VAL* 1.3 78.2 - - - +
28A ALA* 1.3 56.2 + - - +
30A GLY* 2.8 22.5 + - - -
31A HIS 3.6 9.7 + - - +
33A VAL* 3.6 16.9 - - + +
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Residues in contact with ALA 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 GLU* 3.0 21.2 + - + +
25A LEU* 3.6 13.0 - - + +
26A VAL 3.3 0.2 - - - -
27A ALA* 1.3 75.3 - - - +
29A GLY* 1.3 58.3 + - - +
30A GLY* 3.1 4.7 + - - -
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Residues in contact with GLY 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 LEU 3.2 11.2 + - - -
26A VAL 3.3 6.0 + - - -
27A ALA 3.1 1.2 - - - -
28A ALA* 1.3 77.3 - - - +
30A GLY* 1.3 58.1 + - - +
31A HIS* 3.8 10.9 + - - -
145A LEU* 4.3 18.7 - - - +
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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