Contacts of the helix formed by residues 54 - 70 (chain A) in PDB entry 2K7W
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 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A GLN 3.5 4.9 + - - +
53A ASP* 1.3 73.9 + - - +
55A SER* 1.3 60.7 + - - +
56A THR 3.5 0.7 - - - -
57A LYS* 3.4 14.8 - - + +
58A LYS* 2.9 31.9 + - - +
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Residues in contact with SER 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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22A THR* 6.2 2.5 - - - -
53A ASP* 2.7 19.7 + - - -
54A ALA* 1.3 77.1 + - - +
56A THR* 1.3 65.3 + - - +
58A LYS* 3.3 4.0 + - - +
59A LEU* 3.0 33.1 + - - +
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Residues in contact with THR 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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22A THR* 4.1 17.5 - - + -
25A LEU* 3.7 35.2 - - + +
26A LEU* 3.8 33.0 - - + +
51A PRO* 6.1 0.3 - - - +
53A ASP* 2.6 34.9 + - - +
55A SER* 1.3 72.5 - - - +
57A LYS* 1.3 57.4 + - - +
59A LEU* 3.7 1.1 - - + +
60A SER* 2.7 40.6 + - - -
163B TYR* 5.3 2.6 - - - -
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Residues in contact with LYS 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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50A VAL* 5.4 3.0 - - - +
51A PRO* 3.0 44.2 + - + +
52A GLN 5.2 1.2 + - - -
53A ASP 3.6 13.9 + - - +
54A ALA* 3.4 16.2 - - + +
55A SER 3.2 0.2 - - - -
56A THR* 1.3 82.6 + - - +
58A LYS* 1.3 62.7 + - - +
60A SER* 3.4 4.9 + - - -
61A GLU* 3.0 22.6 + - + +
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Residues in contact with LYS 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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54A ALA 2.9 18.1 + - - +
55A SER* 3.8 5.2 - - - +
57A LYS* 1.3 76.2 - - - +
59A LEU* 1.3 63.3 + - + +
61A GLU* 3.1 22.9 + - + +
62A CYS* 3.2 14.3 - - - -
162A LEU* 5.0 19.6 - - + +
165A PHE* 6.3 4.9 - - - -
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Residues in contact with LEU 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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22A THR* 5.6 2.2 - - + -
26A LEU* 3.7 37.5 - - + -
55A SER* 3.0 25.8 + - - +
56A THR* 3.7 1.3 - - + +
58A LYS* 1.3 78.3 - - + +
60A SER* 1.3 61.8 + - - +
62A CYS* 3.0 26.5 - - - -
63A LEU* 3.1 21.5 + - + +
158A TRP* 4.8 15.5 - - + -
161A LEU* 3.9 29.2 - - + -
162A LEU* 3.8 31.4 - - + -
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Residues in contact with SER 60 (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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26A LEU* 4.3 12.6 + - - +
29A GLY* 4.3 10.0 - - - -
30A PHE* 4.3 24.9 + - - +
33A ASP* 6.1 2.7 - - - -
56A THR* 2.7 24.4 + - - -
57A LYS* 3.8 5.8 - - - -
59A LEU* 1.3 75.7 - - - +
61A GLU* 1.3 57.2 + - - +
63A LEU* 3.8 9.0 - - - +
64A LYS* 2.8 35.5 + - - +
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Residues in contact with GLU 61 (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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57A LYS* 3.0 13.7 + - + +
58A LYS* 3.1 16.1 + - + +
60A SER* 1.3 77.4 - - - +
62A CYS* 1.3 63.5 + - - +
64A LYS* 3.3 26.8 + - - +
65A ARG* 2.8 65.2 + - - +
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Residues in contact with CYS 62 (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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58A LYS* 3.2 15.5 - - - +
59A LEU* 3.0 33.2 - - - -
61A GLU* 1.3 78.0 + - - +
63A LEU* 1.3 59.9 + - + +
65A ARG* 3.2 12.8 - - - +
66A ILE* 2.9 40.7 + - + +
165A PHE* 4.2 35.9 - - + -
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Residues in contact with LEU 63 (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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26A LEU* 5.3 11.2 - - + +
30A PHE* 3.6 26.7 - - + -
59A LEU* 3.1 31.2 + - + +
60A SER* 3.8 6.5 - - - +
62A CYS* 1.3 78.3 - - - +
64A LYS* 1.3 57.9 + - - +
66A ILE* 3.8 6.1 - - + +
67A GLY* 2.8 29.5 + - - -
111A VAL* 4.3 24.2 - - + -
114A PHE* 4.7 32.5 - - + -
161A LEU* 5.7 17.0 - - + -
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Residues in contact with LYS 64 (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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30A PHE* 3.6 17.6 - - + -
33A ASP* 2.7 49.4 + - + +
34A ARG* 3.4 23.4 + - - +
60A SER 2.8 22.5 + - - +
61A GLU* 3.3 31.6 + - - +
63A LEU* 1.3 74.3 - - - +
65A ARG* 1.3 68.4 + - + +
67A GLY 3.8 0.3 - - - -
68A ASP* 2.9 31.8 + - + +
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Residues in contact with ARG 65 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A GLU* 2.8 59.0 + - - +
62A CYS* 3.2 18.8 - - - +
64A LYS* 1.3 82.6 - - + +
66A ILE* 1.3 65.8 + - + +
68A ASP* 3.4 5.9 + - - +
69A GLU* 2.9 46.8 + - + +
165A PHE* 5.9 4.9 - - - -
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Residues in contact with ILE 66 (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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62A CYS* 2.9 27.3 + - + +
63A LEU* 4.0 6.5 - - + +
65A ARG* 1.3 79.1 - - + +
67A GLY* 1.3 63.3 + - - +
69A GLU* 3.1 10.1 + - - +
70A LEU* 2.9 46.4 + - + +
111A VAL* 5.2 16.2 - - + -
165A PHE* 4.5 23.8 - - + -
177A VAL* 6.5 1.1 - - + -
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Residues in contact with GLY 67 (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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30A PHE* 5.1 8.3 - - - -
63A LEU 2.8 18.1 + - - -
64A LYS 3.9 0.9 - - - -
66A ILE* 1.3 77.0 - - - +
68A ASP* 1.3 61.2 + - - +
70A LEU* 3.3 10.1 + - - -
71A ASP* 3.7 4.3 + - - +
115A TYR* 3.3 36.5 - - - -
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Residues in contact with ASP 68 (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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34A ARG* 2.8 31.8 + - - +
37A ARG* 5.0 8.1 + - - -
64A LYS* 2.9 19.8 + - + +
65A ARG* 3.6 6.7 - - - +
67A GLY* 1.3 76.3 - - - +
69A GLU* 1.3 65.2 + - - +
71A ASP* 3.2 20.7 + - - +
72A SER* 4.1 3.3 + - - -
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Residues in contact with GLU 69 (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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65A ARG* 2.9 35.6 + - + +
66A ILE* 3.6 10.0 + - - +
68A ASP* 1.3 75.8 - - - +
70A LEU* 1.3 58.8 + - + +
71A ASP 3.0 7.5 + - - -
72A SER* 2.7 29.9 + - - +
73A ASN* 4.2 3.5 - - - +
170A TRP* 5.4 5.9 + - - -
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Residues in contact with LEU 70 (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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66A ILE* 2.9 36.6 + - + +
67A GLY* 3.9 1.3 - - - -
68A ASP 3.2 0.8 - - - -
69A GLU* 1.3 75.5 - - + +
71A ASP* 1.3 56.6 + - - +
72A SER 3.4 0.4 - - - -
73A ASN* 2.8 28.9 + - - +
76A LEU* 4.6 5.9 - - + +
111A VAL* 5.9 3.1 - - + +
115A TYR* 2.8 57.7 + - + -
174A THR* 4.0 32.3 - - + +
177A VAL* 4.3 24.9 - - + -
178A ALA* 5.8 4.0 - - + +
181A LEU* 5.6 0.9 - - + -
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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