Contacts of the helix formed by residues 11 - 26 (chain B) in PDB entry 3KDH
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 11 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B LEU* 1.3 76.1 - - - +
12B ASP* 1.3 65.2 + - - +
13B GLU* 3.6 14.7 + - - +
14B GLU* 2.9 41.9 + - - +
15B GLN* 2.9 21.6 + - - +
42B ARG* 4.2 8.3 - - - +
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Residues in contact with ASP 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B LEU 5.2 1.0 - - - +
11B THR* 1.3 73.4 - - - +
13B GLU* 1.3 68.7 + - - +
15B GLN* 3.3 12.7 + - - +
16B LYS* 2.9 29.8 + - - +
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Residues in contact with GLU 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B THR* 3.2 14.6 + - - +
12B ASP* 1.3 85.8 + - - +
14B GLU* 1.3 65.3 + - + +
16B LYS* 3.3 14.7 + - - +
17B THR* 3.0 28.9 + - - +
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Residues in contact with GLU 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 3.4 18.2 - - + +
11B THR* 2.9 33.6 + - - +
13B GLU* 1.3 77.5 - - + +
15B GLN* 1.3 58.5 + - - +
17B THR* 3.3 1.9 + - - -
18B LEU* 2.9 36.0 + - + +
42B ARG* 2.8 43.1 + - - -
133B PHE* 3.8 25.4 - - + -
142B TYR* 2.6 33.5 + - - +
144B VAL* 4.5 2.0 - - - -
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Residues in contact with GLN 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ALA 2.7 44.6 + - - +
7B VAL* 3.6 29.0 + - + +
10B LEU* 4.4 14.4 + - + +
11B THR 2.9 16.5 + - - +
12B ASP* 3.6 12.5 + - - +
14B GLU* 1.3 76.0 - - - +
16B LYS* 1.3 64.4 + - - +
18B LEU* 3.2 6.1 + - - +
19B GLU* 3.0 22.7 + - - +
22B ILE* 4.9 4.0 - - + +
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Residues in contact with LYS 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ASP 2.9 16.9 + - - +
13B GLU* 3.8 13.4 - - - +
15B GLN* 1.3 77.1 - - - +
17B THR* 1.3 66.9 + - - +
19B GLU* 3.3 27.0 + - - +
20B PRO* 3.8 3.8 - - - +
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Residues in contact with THR 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B GLU 3.0 18.4 + - - -
14B GLU 3.6 4.3 - - - -
16B LYS* 1.3 82.9 - - - +
18B LEU* 1.3 57.5 + - + +
20B PRO* 3.4 17.3 - - - +
21B VAL* 4.8 3.8 - - - +
133B PHE* 3.9 27.5 - - + -
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Residues in contact with LEU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B LEU* 3.6 26.5 - - + -
14B GLU* 2.9 20.5 + - + +
15B GLN* 3.2 3.6 + - - +
17B THR* 1.3 77.6 - - + +
19B GLU* 1.3 65.1 + - - +
20B PRO* 3.3 2.2 - - - -
21B VAL* 2.9 14.6 + - + +
22B ILE* 2.8 35.0 + - + +
131B ASN* 3.6 38.8 - - + +
133B PHE* 3.8 20.2 - - + -
144B VAL* 3.8 19.1 - - + -
146B LEU* 4.2 10.8 - - + -
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Residues in contact with GLU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B GLN* 3.0 12.1 + - + +
16B LYS* 3.4 19.8 - - - +
17B THR 3.3 0.4 - - - -
18B LEU* 1.3 76.4 - - - +
20B PRO* 1.3 65.6 - - + +
22B ILE* 3.3 7.9 + - - +
23B LYS* 2.9 59.6 + - + +
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Residues in contact with PRO 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B LYS 3.8 4.5 - - - +
17B THR 3.4 17.9 - - - +
18B LEU 3.4 0.4 - - - -
19B GLU* 1.3 97.1 - - + +
21B VAL* 1.3 56.2 + - + +
23B LYS* 3.9 6.8 - - + +
24B THR* 2.7 38.9 + - - +
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Residues in contact with VAL 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B THR 4.8 3.4 - - - +
18B LEU* 2.9 23.6 + - + +
20B PRO* 1.3 78.1 - - + +
22B ILE* 1.3 65.4 + - - +
24B THR* 4.6 0.7 - - - -
25B TYR* 3.0 43.2 + - + -
26B HIS* 3.7 4.5 - - + -
109B VAL* 5.9 0.2 - - + -
129B SER* 3.6 25.6 - - - +
131B ASN* 3.6 21.1 - - - +
146B LEU* 4.1 9.0 - - + -
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Residues in contact with ILE 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B VAL* 4.3 21.1 - - + -
15B GLN* 4.9 6.1 - - + +
18B LEU* 2.8 34.2 + - + +
19B GLU* 3.7 7.6 - - + +
21B VAL* 1.3 76.2 - - - +
23B LYS* 1.3 61.5 + - + +
26B HIS* 2.9 46.6 + - + +
27B GLN* 4.5 0.3 - - - -
38B LEU* 4.1 28.3 - - + -
146B LEU* 3.7 21.3 - - + -
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Residues in contact with LYS 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B GLU* 2.9 48.0 + - + +
20B PRO* 4.0 6.3 - - + +
22B ILE* 1.3 80.6 - - + +
24B THR* 1.3 59.3 + - - +
27B GLN* 2.7 46.2 + - - +
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Residues in contact with THR 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B PRO* 2.7 24.7 + - - +
23B LYS* 1.3 80.1 - - - +
25B TYR* 1.3 95.2 + - + +
27B GLN* 5.0 2.9 - - - +
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Residues in contact with TYR 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B VAL* 3.0 34.4 + - + +
24B THR* 1.3 103.2 - - + +
26B HIS* 1.3 71.8 + - + +
27B GLN* 3.6 3.5 + - - +
102B PHE* 4.7 16.2 - + - -
104B ASP* 4.3 4.0 + - - -
107B HIS* 3.2 38.5 + + + -
109B VAL* 3.9 39.7 - - + -
127B VAL* 3.5 32.8 - - + +
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Residues in contact with HIS 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B VAL* 3.7 15.5 - - + -
22B ILE* 2.9 34.5 + - + +
25B TYR* 1.3 82.2 - - + +
27B GLN* 1.3 64.2 + - - +
28B PHE* 3.7 7.3 + - - +
38B LEU* 4.1 9.7 - - + +
127B VAL* 3.3 34.0 + - + +
129B SER* 2.9 29.8 + - - -
146B LEU* 3.4 30.5 - - + +
148B SER* 2.8 37.2 + - - +
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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