Contacts of the helix formed by residues 24 - 35 (chain P) in PDB entry 1KD1
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 ALA 24 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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709A G 3.4 22.0 + - - +
710A G 2.9 29.1 + - - +
18P ALA* 5.2 0.4 - - - -
22P GLY 4.5 2.9 - - - +
23P GLY* 1.3 73.5 - - - +
25P VAL* 1.3 67.7 + - - +
26P TRP 3.3 1.6 - - - -
27P GLY* 3.5 4.4 + - - +
28P ASP* 3.0 22.4 + - - +
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Residues in contact with VAL 25 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709A G 2.8 36.1 - - + +
710A G 3.8 1.3 - - - -
24P ALA* 1.3 79.3 - - - +
26P TRP* 1.3 82.9 + - + +
28P ASP* 3.0 8.2 + - - +
29P VAL* 2.7 42.1 + - + +
59P VAL* 5.8 0.2 - - + -
108P GLY* 3.6 33.4 - - - +
111P VAL* 3.6 26.2 - - + -
113P VAL* 4.5 7.6 - - + -
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Residues in contact with TRP 26 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14P LEU* 3.3 45.2 - - + +
17P ALA* 3.7 17.7 - - + -
18P ALA* 3.9 8.5 - - + -
23P GLY* 4.7 3.6 - - - -
24P ALA 3.3 1.0 - - - +
25P VAL* 1.3 95.5 - - + +
27P GLY* 1.3 56.4 + - - +
29P VAL* 3.3 5.3 + - + +
30P ALA* 2.9 28.9 + - - +
57P THR* 6.2 1.1 - - + -
59P VAL* 4.1 35.2 - - + -
98P LEU* 4.7 8.1 - - + -
101P ALA* 3.9 31.4 - - + -
102P ILE* 4.2 8.4 - - + +
105P ASN* 3.2 32.4 + - + -
106P PRO* 3.4 21.9 + - - +
108P GLY* 3.7 15.4 - - - +
111P VAL* 5.3 2.5 - - + -
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Residues in contact with GLY 27 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14P LEU 4.6 0.7 - - - -
15P LYS* 5.4 2.5 - - - -
18P ALA* 3.2 21.5 - - - +
24P ALA 3.5 5.5 + - - -
25P VAL 3.3 0.2 - - - -
26P TRP* 1.3 79.2 - - - +
28P ASP* 1.3 63.1 + - - +
30P ALA* 3.4 7.3 - - - +
31P GLU* 3.1 34.8 + - - +
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Residues in contact with ASP 28 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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708A A 2.8 33.3 + - - +
709A G 3.8 16.0 + - - +
24P ALA 3.0 13.3 + - - +
25P VAL* 3.0 13.8 + - - +
27P GLY* 1.3 78.9 - - - +
29P VAL* 1.3 62.6 + - + +
31P GLU* 3.3 12.7 + - - +
32P ARG* 3.2 21.1 + - - +
113P VAL* 5.7 7.4 - - + +
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Residues in contact with VAL 29 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14P LEU* 3.9 12.8 - - + -
25P VAL* 2.7 29.9 + - + +
26P TRP* 3.7 10.1 - - + +
28P ASP* 1.3 71.4 - - + +
30P ALA* 1.3 66.2 + - - +
32P ARG* 3.4 5.4 + - - +
33P LEU* 3.0 30.8 + - + +
59P VAL* 3.9 24.9 - - + -
61P PRO* 4.1 20.0 - - + -
98P LEU* 3.9 27.6 - - + -
113P VAL* 5.4 6.3 - - + -
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Residues in contact with ALA 30 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11P ILE* 4.3 8.2 - - + +
14P LEU* 4.1 22.2 - - + +
15P LYS* 4.1 23.6 - - + +
26P TRP 2.9 17.3 + - - +
27P GLY* 3.4 10.3 - - - +
29P VAL* 1.3 79.0 - - - +
31P GLU* 1.3 57.7 + - + +
33P LEU* 3.2 4.4 + - - +
34P GLU* 3.0 33.7 + - - +
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Residues in contact with GLU 31 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27P GLY* 3.1 21.8 + - - +
28P ASP* 3.7 11.2 + - - +
29P VAL 3.3 0.2 - - - -
30P ALA* 1.3 79.2 - - + +
32P ARG* 1.3 61.2 + - - +
34P GLU* 3.3 17.7 + - - +
35P LYS* 3.3 30.1 + - - +
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Residues in contact with ARG 32 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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936A C 3.1 27.8 + - - -
937A C 5.2 5.1 + - - -
28P ASP 3.2 13.7 + - - +
29P VAL* 3.9 4.0 - - - +
30P ALA 3.3 0.2 - - - -
31P GLU* 1.3 78.5 - - - +
33P LEU* 1.3 60.7 + - - +
35P LYS* 3.1 31.7 + - - +
39P THR* 3.8 27.7 + - - +
40P HIS* 3.0 16.6 + - + +
61P PRO* 4.0 32.5 - - + +
115P ARG* 3.6 28.6 - - - +
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Residues in contact with LEU 33 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2P LYS* 3.4 10.6 - - - -
7P LEU* 4.2 13.7 - - + +
10P LEU* 4.2 6.5 - - + -
11P ILE* 3.8 21.8 - - + +
14P LEU* 3.8 26.9 - - + -
29P VAL* 3.0 23.0 + - + +
30P ALA 3.7 4.5 - - - +
32P ARG* 1.3 75.0 - - - +
34P GLU* 1.3 63.1 + - - +
35P LYS 3.2 1.0 - - - +
40P HIS* 2.9 36.1 + - + +
61P PRO* 3.7 26.0 - - + +
62P GLY* 4.8 0.4 - - - -
79P VAL* 3.8 28.7 - - + -
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Residues in contact with GLU 34 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655A U 4.8 0.7 + - - -
1279A U 5.4 3.5 - - - +
2P LYS* 3.7 15.8 + - + +
11P ILE* 4.0 17.5 - - + +
15P LYS* 3.2 33.4 + - - -
30P ALA 3.0 18.0 + - - +
31P GLU* 3.5 22.2 - - - +
32P ARG 3.2 0.2 - - - -
33P LEU* 1.3 77.6 - - - +
35P LYS* 1.3 61.2 + - + +
36P PRO* 4.5 1.2 - - - +
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Residues in contact with LYS 35 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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935A G 4.9 4.0 - - - +
936A C 2.9 38.5 + - - +
937A C 5.3 3.8 + - - -
2P LYS* 3.1 8.9 + - - -
31P GLU* 3.3 16.6 - - - +
32P ARG* 3.1 35.4 + - - +
33P LEU 3.0 1.2 - - - -
34P GLU* 1.3 79.6 - - + +
36P PRO* 1.3 71.8 - - + +
39P THR* 3.6 9.0 - - + +
40P HIS* 2.6 27.1 + - - -
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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