Contacts of the helix formed by residues 53 - 69 (chain A) in PDB entry 5HK1
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 ASP 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A GLY 4.1 0.2 + - - -
52A LEU* 1.3 73.0 - - - +
54A HIS* 1.3 60.5 + - + +
55A GLU* 3.2 11.5 - - + +
56A LEU* 3.0 47.2 + - - +
57A ALA 2.9 24.1 + - - -
304A SO4 3.3 22.7 - - - +
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Residues in contact with HIS 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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52A LEU 3.5 1.3 + - - -
53A ASP* 1.3 72.6 - - + +
55A GLU* 1.3 78.8 + - + +
57A ALA* 3.6 8.6 - - - +
58A PHE* 2.8 52.1 + + + -
129A ILE* 4.3 8.1 - - + -
130A SER* 4.3 4.3 - - - +
167A ASN* 3.9 15.5 - - - -
169A TRP* 3.8 34.0 + + + -
304A SO4 2.8 42.1 + - - +
141B THR* 3.2 37.1 + - - -
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Residues in contact with GLU 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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53A ASP* 3.1 10.4 + - + +
54A HIS* 1.3 92.5 - - + +
56A LEU* 1.3 61.4 + - - +
58A PHE* 3.5 9.5 + - - +
59A SER* 3.2 21.0 + - - -
81A TRP* 5.4 1.0 + - - -
141B THR* 2.4 39.3 + - - +
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Residues in contact with LEU 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 LEU* 4.4 21.3 - - + -
53A ASP* 3.0 30.7 + - - +
55A GLU* 1.3 72.3 - - - +
57A ALA* 1.3 61.4 + - - +
59A SER* 3.2 10.4 + - - +
60A ARG* 2.9 52.6 + - + +
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Residues in contact with ALA 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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49A TYR* 3.3 41.3 - - + +
52A LEU* 4.2 4.4 - - + +
53A ASP 2.9 16.0 + - - +
54A HIS* 3.6 10.3 - - - +
56A LEU* 1.3 77.5 - - - +
58A PHE* 1.3 61.8 + - - +
60A ARG* 3.5 4.1 + - - +
61A LEU* 3.0 25.6 + - - +
129A ILE* 4.1 16.2 - - + -
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Residues in contact with PHE 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 HIS* 2.8 41.4 + + + +
55A GLU* 3.6 12.3 - - - +
57A ALA* 1.3 73.6 - - - +
59A SER* 1.3 61.9 + - - +
61A LEU* 3.3 4.9 + - + +
62A ILE* 3.0 31.9 + - + +
81A TRP* 3.8 26.0 - + - -
106A LEU* 3.5 43.2 - - + +
107A PHE 4.8 1.8 - - - -
129A ILE* 3.4 29.2 - - + -
169A TRP* 3.7 37.2 - + + -
170A MET 4.6 2.7 - - - -
141B THR* 4.9 0.9 - - + -
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Residues in contact with SER 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 GLU 3.2 9.7 + - - -
56A LEU* 3.2 17.5 + - - +
58A PHE* 1.3 80.8 - - - +
60A ARG* 1.3 62.8 + - - +
62A ILE* 3.4 8.1 + - - +
63A VAL* 3.1 35.4 + - - +
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Residues in contact with ARG 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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49A TYR* 3.8 37.1 + - + -
52A LEU* 4.2 19.4 - - + +
56A LEU* 2.9 36.7 + - + +
57A ALA 3.8 4.5 - - - +
59A SER* 1.3 75.5 - - - +
61A LEU* 1.3 57.5 + - - +
63A VAL* 3.8 5.4 - - - +
64A GLU* 3.0 29.3 + - - +
307A SO4 3.0 38.8 + - - -
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Residues in contact with LEU 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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42A ILE* 4.9 1.8 - - + +
45A LEU* 4.0 15.9 - - + +
46A ALA* 3.7 28.3 - - + +
49A TYR* 3.6 12.6 - - + -
57A ALA 3.0 18.0 + - - +
58A PHE* 3.7 4.9 - - + +
60A ARG* 1.3 75.2 - - - +
62A ILE* 1.3 60.6 + - - +
64A GLU* 3.3 2.6 + - - +
65A LEU* 2.8 56.8 + - + +
96A LEU* 4.2 14.1 - - + -
106A LEU* 4.2 12.1 - - + -
129A ILE* 5.4 2.7 - - + -
171A VAL* 3.7 31.2 - - + -
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Residues in contact with ILE 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 PHE* 3.0 26.1 + - + +
59A SER* 3.8 6.7 - - - +
61A LEU* 1.3 78.4 - - + +
63A VAL* 1.3 63.3 + - + +
65A LEU* 3.3 8.2 + - - +
66A ARG* 3.0 57.6 + - - +
73A VAL* 4.5 9.4 - - + -
79A LEU* 4.0 16.4 - - + -
94A CYS* 5.7 1.8 - - - -
96A LEU* 3.9 33.2 - - + -
106A LEU* 4.3 14.1 - - + -
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Residues in contact with VAL 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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59A SER* 3.1 24.0 + - - +
60A ARG* 3.8 6.7 - - - +
62A ILE* 1.3 78.7 - - + +
64A GLU* 1.3 65.3 + - - +
66A ARG* 3.3 15.3 + - - +
67A ARG* 3.3 24.8 + - + +
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Residues in contact with GLU 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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45A LEU* 3.6 32.2 - - + +
49A TYR* 3.7 14.2 + - - +
60A ARG 3.0 18.8 + - - +
61A LEU* 3.7 4.7 - - - +
63A VAL* 1.3 75.8 - - - +
65A LEU* 1.3 65.5 + - - +
67A ARG* 2.4 48.8 + - - +
68A LEU* 3.2 33.9 + - + +
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Residues in contact with LEU 65 (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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37A PHE* 4.0 18.4 - - + -
41A GLU* 5.2 2.2 - - - +
42A ILE* 3.9 22.2 - - + -
45A LEU* 3.6 23.1 - - + -
61A LEU* 2.8 41.4 + - + +
62A ILE* 3.3 5.6 + - - +
64A GLU* 1.3 76.2 - - - +
66A ARG* 1.3 57.5 + - - +
68A LEU* 3.9 2.1 - - + +
69A HIS* 2.9 38.7 + - + +
73A VAL* 3.9 17.6 - - + +
96A LEU* 4.1 18.4 - - + -
104A VAL* 4.1 15.3 - - + -
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Residues in contact with ARG 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 ILE* 3.0 40.5 + - - +
63A VAL* 3.6 16.5 - - - +
64A GLU 3.3 0.2 - - - -
65A LEU* 1.3 78.1 - - - +
67A ARG* 1.3 57.2 + - - +
69A HIS 4.4 1.3 - - - -
70A PRO* 3.0 33.6 - - + +
73A VAL* 3.8 26.5 - - + +
74A LEU 2.4 35.4 + - - -
75A PRO* 3.6 8.7 - - - +
76A ASP* 2.1 33.3 + - - +
79A LEU* 4.2 2.8 - - - +
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Residues in contact with ARG 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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63A VAL* 3.3 12.8 + - + +
64A GLU* 2.4 62.2 + - - +
66A ARG* 1.3 77.5 - - - +
68A LEU* 1.3 80.8 + - - +
70A PRO* 3.8 8.6 - - - +
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Residues in contact with LEU 68 (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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41A GLU* 3.7 19.7 - - + +
45A LEU* 4.2 23.1 - - + -
64A GLU* 3.2 32.6 + - + +
65A LEU* 3.9 2.5 - - + +
67A ARG* 1.3 103.6 - - - +
69A HIS* 1.3 83.0 + - + +
70A PRO* 3.6 4.4 - - - +
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Residues in contact with HIS 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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36A VAL* 3.2 30.9 + - + +
37A PHE* 3.5 25.8 - + + -
41A GLU* 2.6 36.8 + - - -
65A LEU* 2.9 17.2 + - + +
66A ARG* 3.4 4.0 - - - +
68A LEU* 1.3 95.7 + - + +
70A PRO* 1.3 66.4 - - - +
71A GLY 3.4 0.2 + - - -
72A HIS* 3.3 32.4 + - + +
73A VAL* 4.1 6.2 + - - +
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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