Contacts of the helix formed by residues 46 - 59 (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 SER 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A PHE 4.1 1.0 + - - -
45A PHE* 1.3 75.9 - - - +
47A LEU* 1.3 64.5 + - - +
48A GLU* 3.5 5.2 + - - +
49A GLU* 2.9 39.7 + - - +
50A ARG* 2.9 21.4 + - - -
156A LYS* 4.1 4.0 - - - +
169A PG4 3.4 30.1 + - - -
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Residues in contact with LEU 47 (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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35A VAL* 3.4 43.3 - - + +
36A ALA 4.2 8.3 - - - +
37A ASP* 3.5 31.4 - - + +
46A SER* 1.3 72.3 - - - +
48A GLU* 1.3 61.8 + - - +
50A ARG* 3.2 10.0 + - - +
51A LEU* 2.9 37.7 + - + +
68A GLY* 4.3 4.5 - - - -
69A PHE 4.5 9.6 - - - +
70A THR* 4.4 15.5 - - + -
169A PG4 3.1 25.0 + - - -
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Residues in contact with GLU 48 (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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46A SER* 3.2 5.3 - - - +
47A LEU* 1.3 75.4 - - - +
49A GLU* 1.3 64.5 + - + +
51A LEU* 3.4 10.3 + - - +
52A LYS* 3.1 53.4 + - + +
169A PG4 3.1 36.8 + - - +
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Residues in contact with GLU 49 (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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45A PHE* 3.4 20.0 - - + -
46A SER* 2.9 30.2 + - - +
48A GLU* 1.3 78.4 - - + +
50A ARG* 1.3 56.5 + - - +
52A LYS* 3.1 9.2 + - + +
53A ILE* 2.8 36.0 + - - +
152A TRP* 3.8 27.2 - - + -
156A LYS* 2.8 37.2 + - - +
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Residues in contact with ARG 50 (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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9A THR* 2.9 32.2 + - - +
10A PHE* 3.3 21.0 - - - +
11A ASP* 3.8 16.2 - - - +
13A LEU* 6.0 0.2 - - - +
35A VAL* 3.7 18.3 - - + +
36A ALA 2.8 22.8 + - - -
37A ASP 2.8 24.8 + - - -
43A PRO* 3.8 8.3 - - - +
45A PHE* 2.8 32.7 + - + -
46A SER 2.9 12.0 + - - +
47A LEU* 3.4 23.6 - - - +
49A GLU* 1.3 74.6 - - - +
51A LEU* 1.3 57.6 + - - +
53A ILE* 3.7 8.2 - - + +
54A ALA* 3.0 30.8 + - - +
169A PG4 3.0 21.0 + - - -
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Residues in contact with LEU 51 (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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35A VAL* 3.7 22.7 - - + -
47A LEU* 2.9 41.2 + - + +
48A GLU* 3.6 8.7 - - - +
50A ARG* 1.3 73.9 - - - +
52A LYS* 1.3 59.7 + - + +
54A ALA* 3.4 3.0 + - - +
55A ASN* 2.9 41.9 + - - +
66A VAL* 3.8 12.5 - - + +
67A MET* 3.7 5.6 - - - -
68A GLY* 3.5 31.0 - - - +
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Residues in contact with LYS 52 (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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48A GLU* 3.1 48.0 + - + +
49A GLU* 3.6 6.9 - - + +
51A LEU* 1.3 75.0 - - + +
53A ILE* 1.3 63.5 + - - +
55A ASN* 3.3 6.4 + - - +
56A GLU* 3.0 34.9 + - - +
152A TRP* 3.9 32.4 - - + -
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Residues in contact with ILE 53 (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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10A PHE 5.8 0.2 - - - +
12A PRO* 4.2 11.2 - - + -
13A LEU* 4.3 9.6 - - + +
45A PHE* 3.8 40.8 - - + -
49A GLU 2.8 22.3 + - - +
50A ARG* 3.7 7.6 - - - +
52A LYS* 1.3 78.6 - - - +
54A ALA* 1.3 62.3 + - - +
56A GLU* 3.3 11.4 + - - +
57A VAL* 3.4 15.9 + - - +
148A SER* 5.0 0.2 + - - -
149A VAL* 3.8 33.2 - - + +
152A TRP* 3.4 43.3 - - + +
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Residues in contact with ALA 54 (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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10A PHE* 5.6 2.5 - - + -
13A LEU* 4.3 23.1 - - + -
33A VAL* 5.3 1.8 - - + -
35A VAL* 4.8 7.6 - - + -
50A ARG 3.0 18.6 + - - +
51A LEU 3.9 2.9 - - - +
53A ILE* 1.3 75.3 - - - +
55A ASN* 1.3 58.1 + - - +
57A VAL* 3.2 1.7 + - - -
58A LEU* 2.9 46.7 + - + +
66A VAL* 4.0 19.3 - - + -
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Residues in contact with ASN 55 (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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51A LEU* 2.9 29.6 + - - +
52A LYS* 3.8 7.3 - - - +
54A ALA* 1.3 73.2 - - - +
56A GLU* 1.3 62.2 + - + +
59A GLY* 2.9 35.6 + - - +
66A VAL* 3.3 34.6 + - - +
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Residues in contact with GLU 56 (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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52A LYS* 3.0 22.0 + - + +
53A ILE* 3.6 5.3 - - - +
54A ALA 3.3 0.4 - - - -
55A ASN* 1.3 78.2 - - + +
57A VAL* 1.3 60.5 + - - +
59A GLY* 4.5 1.2 + - - -
60A HIS* 5.5 1.7 + - - -
148A SER* 3.7 25.4 + - - +
152A TRP* 3.0 42.7 + - - -
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Residues in contact with VAL 57 (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* 3.6 27.8 - - + -
18A GLU* 3.7 23.5 - - + +
53A ILE 3.4 12.8 + - - +
54A ALA 3.2 2.7 + - - +
56A GLU* 1.3 77.1 - - - +
58A LEU* 1.3 60.6 + - + +
59A GLY 3.6 0.4 - - - -
60A HIS* 3.2 24.6 + - - -
61A TYR* 4.8 0.2 - - - -
146A PHE* 3.8 22.4 - - + -
148A SER* 3.6 20.0 - - - +
149A VAL* 3.7 19.7 - - + -
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Residues in contact with LEU 58 (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* 3.9 26.0 - - + -
18A GLU* 3.9 27.6 - - + -
21A VAL* 3.9 28.7 - - + -
33A VAL* 4.0 27.4 - - + -
54A ALA* 2.9 22.2 + - + +
57A VAL* 1.3 77.6 - - - +
59A GLY* 1.3 64.4 + - - +
60A HIS 3.1 3.1 - - - -
61A TYR* 3.0 32.7 + - + +
64A VAL* 4.4 10.4 - - + +
66A VAL* 4.1 16.8 - - + -
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Residues in contact with GLY 59 (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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55A ASN* 2.9 24.8 + - - +
56A GLU 4.5 1.4 + - - -
57A VAL 3.6 1.2 - - - -
58A LEU* 1.3 76.6 - - - +
60A HIS* 1.3 60.3 + - - +
61A TYR 3.4 6.6 + - - +
62A PRO* 5.4 0.5 - - - +
64A VAL 5.6 1.5 - - - +
66A VAL* 6.3 0.2 - - - -
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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