Contacts of the helix formed by residues 11 - 26 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10C LEU* 1.3 73.4 - - - +
12C ASP* 1.3 65.0 + - - +
13C GLU* 3.3 16.3 + - - +
14C GLU* 3.0 40.9 + - - +
15C GLN* 2.9 26.3 + - - +
42C ARG* 4.4 7.4 - - - +
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Residues in contact with ASP 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C LEU 4.9 0.5 - - - +
11C THR* 1.3 74.6 - - - +
13C GLU* 1.3 68.6 + - - +
15C GLN* 3.3 19.6 + - - +
16C LYS* 2.9 29.7 + - - +
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Residues in contact with GLU 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C THR* 3.3 20.4 + - - +
12C ASP* 1.3 85.3 + - + +
14C GLU* 1.3 60.1 + - + +
16C LYS* 3.3 9.4 + - - +
17C THR* 2.9 33.6 + - - +
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Residues in contact with GLU 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C LEU* 3.5 17.7 - - + +
11C THR* 3.0 35.5 + - - +
13C GLU* 1.3 75.6 - - + +
15C GLN* 1.3 58.0 + - - +
17C THR* 3.1 2.8 + - - -
18C LEU* 2.8 37.0 + - + +
42C ARG* 2.9 42.5 + - - -
133C PHE* 4.0 23.3 - - + -
142C TYR* 2.6 32.8 + - - +
144C VAL* 4.5 2.2 - - - -
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Residues in contact with GLN 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C VAL* 4.1 37.6 + - + +
9C GLY 5.9 0.2 - - - +
10C LEU* 3.2 37.5 + - + +
11C THR 2.9 25.4 + - - +
12C ASP* 3.5 17.4 + - - +
14C GLU* 1.3 76.8 - - - +
16C LYS* 1.3 63.0 + - - +
18C LEU* 3.2 5.8 + - - +
19C GLU* 3.0 22.9 + - - +
22C ILE* 5.3 2.3 - - - +
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Residues in contact with LYS 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C ASP 2.9 16.8 + - - +
13C GLU* 3.7 8.7 - - - +
14C GLU 3.3 0.2 - - - -
15C GLN* 1.3 75.6 - - - +
17C THR* 1.3 64.3 + - - +
19C GLU* 3.2 28.7 + - - +
20C PRO* 3.9 2.8 - - - +
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Residues in contact with THR 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C GLU* 2.9 16.2 + - - +
14C GLU 3.1 8.0 + - - -
16C LYS* 1.3 79.0 - - - +
18C LEU* 1.3 58.8 + - + +
20C PRO* 3.4 16.3 - - - +
21C VAL* 4.8 3.6 - - - +
131C ASN* 6.3 0.9 - - - +
132C GLU 6.1 0.4 - - - +
133C PHE* 3.8 29.0 - - + -
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Residues in contact with LEU 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C LEU* 3.7 28.9 - - + -
14C GLU* 2.8 17.4 + - + +
15C GLN* 3.2 4.5 + - - +
17C THR* 1.3 77.4 - - + +
19C GLU* 1.3 65.8 + - - +
20C PRO* 3.3 3.6 - - - -
21C VAL* 3.1 12.0 + - + +
22C ILE* 3.0 34.0 + - + +
131C ASN* 3.7 38.8 - - + +
133C PHE* 3.9 17.9 - - + -
144C VAL* 3.8 21.3 - - + -
146C LEU* 4.2 14.8 - - + -
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Residues in contact with GLU 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C GLN 3.0 10.7 + - - +
16C LYS* 3.4 20.7 - - - +
18C LEU* 1.3 77.1 - - - +
20C PRO* 1.3 64.8 - - + +
22C ILE* 3.2 8.6 + - - +
23C LYS* 2.9 39.3 + - + +
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Residues in contact with PRO 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C LYS 3.9 3.6 - - - +
17C THR 3.4 13.7 - - - +
18C LEU 3.3 4.3 - - - -
19C GLU* 1.3 98.5 - - + +
21C VAL* 1.3 59.2 + - + +
23C LYS* 3.4 7.4 + - + +
24C THR* 2.9 35.2 + - - +
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Residues in contact with VAL 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C THR 4.8 3.8 - - - +
18C LEU* 3.1 21.9 + - + +
20C PRO* 1.3 75.4 - - + +
22C ILE* 1.3 61.3 + - - +
24C THR* 3.2 1.2 + - - -
25C TYR* 2.9 46.8 + - + +
26C HIS* 3.8 1.2 - - + -
109C VAL* 5.7 0.4 - - + -
129C SER* 3.5 30.5 - - - +
131C ASN* 3.7 33.9 - - - +
146C LEU* 4.3 7.0 - - + -
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Residues in contact with ILE 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C SER* 4.0 7.0 - - - +
5C PRO* 3.6 30.3 - - + -
7C VAL* 3.6 35.0 - - + -
10C LEU* 5.8 0.2 - - + -
15C GLN* 5.3 3.1 - - - +
18C LEU* 3.0 25.8 + - + +
19C GLU* 3.7 8.7 - - - +
21C VAL* 1.3 75.6 - - - +
23C LYS* 1.3 61.3 + - - +
26C HIS* 2.9 35.1 + - + -
27C GLN* 3.0 12.7 + - - +
38C LEU* 4.0 11.9 - - + -
146C LEU* 3.7 23.8 - - + -
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Residues in contact with LYS 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C SER* 3.5 28.6 + - - +
19C GLU* 2.9 27.2 + - + +
20C PRO* 3.8 7.9 - - + +
22C ILE* 1.3 76.8 - - + +
24C THR* 1.3 60.9 + - - +
27C GLN* 3.1 39.7 + - - +
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Residues in contact with THR 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C PRO* 2.9 21.9 + - - +
21C VAL* 4.7 0.2 - - - -
23C LYS* 1.3 80.6 - - - +
25C TYR* 1.3 99.3 + - + +
26C HIS 3.8 0.2 - - - -
27C GLN* 5.2 2.1 + - - +
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Residues in contact with TYR 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C VAL* 2.9 31.8 + - + +
24C THR* 1.3 103.7 - - + +
26C HIS* 1.3 72.2 + - + +
27C GLN 3.7 2.7 + - - +
102C PHE* 4.3 19.2 - + - -
104C ASP* 4.3 4.5 + - - -
107C HIS* 3.4 36.2 + + + +
109C VAL* 3.7 40.4 - - + -
127C VAL* 3.6 31.7 - - + +
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Residues in contact with HIS 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C PRO* 2.9 23.1 - - + +
21C VAL 3.8 15.0 - - - -
22C ILE* 2.9 29.9 + - + +
25C TYR* 1.3 82.0 + - + +
27C GLN* 1.3 64.1 + - - +
28C PHE* 5.0 0.3 - - - +
38C LEU* 4.0 9.8 - - + +
127C VAL* 3.3 30.3 - - + +
129C SER* 2.9 31.8 + - - -
146C LEU* 3.4 32.7 - - + +
148C SER* 2.8 37.3 + - - +
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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