Contacts of the helix formed by residues 63 - 76 (chain D) in PDB entry 5HK5
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 63 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87B PRO* 6.1 0.5 - - - +
90B LEU* 4.8 12.1 - - + +
111B ASP* 4.1 26.5 - - + +
61D GLU 3.8 0.2 + - - -
62D PRO* 1.3 77.1 - - - +
64D ASN* 1.3 65.2 + - - +
65D HIS* 3.9 9.4 + - - +
66D ALA* 2.9 40.5 + - - +
67D VAL* 2.9 11.8 + - - +
120D ARG* 3.6 37.1 + - - +
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Residues in contact with ASN 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B TYR* 4.0 10.1 - - - +
110B GLU* 2.7 36.8 + - - +
111B ASP* 3.5 7.0 + - - +
112B MET* 3.5 12.8 - - - -
62D PRO 3.7 2.2 + - - +
63D THR* 1.3 71.7 - - - +
65D HIS* 1.3 63.3 + - - +
67D VAL* 3.2 12.2 + - - +
68D ILE* 3.0 28.1 + - - +
52G VAL 4.7 0.5 - - - +
53G LEU* 3.6 16.3 - - + +
54G ALA* 3.1 46.5 + - - +
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Residues in contact with HIS 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 4.8 3.4 - - + +
43B TYR* 5.0 0.7 - - - -
45B ALA* 3.8 12.2 - - + +
46B PHE 2.8 26.5 + - - -
47B HIS* 4.3 2.7 - - - -
87B PRO* 4.1 13.0 - - + +
90B LEU* 3.9 12.6 - - + -
111B ASP 2.8 21.4 + - - +
112B MET* 3.5 21.8 - - - +
114B VAL* 3.3 29.7 - - + +
63D THR* 3.9 3.8 - - - +
64D ASN* 1.3 76.2 - - - +
66D ALA* 1.3 58.2 + - - +
68D ILE* 3.2 8.1 + - + +
69D GLN* 2.9 53.6 + - + +
120D ARG 4.4 3.4 + - - -
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Residues in contact with ALA 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D LEU* 4.5 2.2 - - + -
62D PRO* 4.1 4.9 - - + -
63D THR* 2.9 27.6 + - - +
65D HIS* 1.3 73.8 - - - +
67D VAL* 1.3 63.4 + - - +
70D THR* 2.6 33.5 + - - +
83D THR* 3.5 20.1 - - + +
119D CYS* 3.5 24.9 - - + +
120D ARG* 4.0 8.3 - - - +
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Residues in contact with VAL 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B TRP* 4.7 9.0 - - + -
56D LEU* 4.2 6.7 - - + -
62D PRO* 3.8 15.7 - - + +
63D THR 2.9 16.1 + - - +
64D ASN* 3.4 11.0 - - - +
66D ALA* 1.3 77.7 - - - +
68D ILE* 1.3 65.1 + - - +
70D THR* 3.7 1.9 - - - -
71D LEU* 3.0 22.9 + - + +
33G PRO* 3.5 31.5 - - + +
34G TYR* 3.6 22.9 - - - +
52G VAL 3.7 21.5 - - - +
53G LEU* 4.7 6.7 - - + -
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Residues in contact with ILE 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 5.6 1.3 - - + -
26B VAL* 3.7 32.8 - - + -
28B PHE* 4.1 9.4 - - + -
31B MET* 3.8 13.2 - - + +
33B TRP* 4.0 26.5 - - + -
43B TYR* 3.7 22.2 - - + +
45B ALA* 5.7 0.7 - - + -
112B MET* 3.8 19.7 - - + -
64D ASN 3.0 17.5 + - - +
65D HIS* 3.2 8.7 + - + +
67D VAL* 1.3 75.5 - - - +
69D GLN* 1.3 58.7 + - - +
71D LEU* 3.3 6.9 + - - +
72D MET* 3.0 31.7 + - - +
53G LEU* 4.6 3.4 - - + -
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Residues in contact with GLN 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 4.4 12.3 - - + +
47B HIS* 4.0 21.2 - - - +
48B CYS 4.8 5.4 + - - -
87B PRO* 5.6 0.9 - - - +
65D HIS* 2.9 41.1 + - + +
68D ILE* 1.3 75.1 - - - +
70D THR* 1.3 60.7 + - - +
72D MET* 3.4 6.5 + - - +
73D ASN* 2.9 29.0 + - - +
80D THR* 3.8 11.6 - - + +
81D PRO* 3.1 32.8 + - - +
82D PRO 3.9 10.5 + - - -
83D THR* 4.0 17.9 - - + +
120D ARG 4.4 4.2 - - - +
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Residues in contact with THR 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D CYS 3.7 13.0 - - - +
53D GLU* 4.7 0.7 - - - -
54D PHE* 3.7 23.3 - - + +
56D LEU* 3.7 31.2 - - + +
66D ALA 2.6 22.9 + - - -
67D VAL 3.7 2.7 - - - -
69D GLN* 1.3 75.5 - - - +
71D LEU* 1.3 63.5 + - - +
73D ASN* 3.3 9.3 + - + +
74D SER* 3.0 22.9 + - - -
82D PRO* 5.6 0.7 - - - -
83D THR* 3.2 24.8 + - - +
33G PRO* 4.8 4.9 - - + -
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Residues in contact with LEU 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B MET* 3.7 16.6 - - + +
33B TRP* 3.6 34.3 - - + +
54D PHE* 4.2 15.0 - - + -
67D VAL 3.0 13.5 + - - +
68D ILE 3.5 10.1 - - - +
70D THR* 1.3 77.9 - - - +
72D MET* 1.3 60.4 + - - +
74D SER* 2.7 23.8 + - - +
75D MET* 3.3 17.3 + - - +
93E LEU* 3.1 34.5 - - + -
31G PRO* 3.8 16.8 - - + +
32G SER 4.5 2.5 - - - -
33G PRO* 4.5 14.5 - - + +
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Residues in contact with MET 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 3.6 42.8 - - + -
25B HIS 3.7 17.3 - - - +
26B VAL* 4.3 13.0 - - - -
27B ASN 5.5 0.9 - - - +
31B MET* 4.3 9.9 - - + +
68D ILE* 3.0 30.1 + - - +
69D GLN 3.7 4.5 - - - +
71D LEU* 1.3 74.6 - - - +
73D ASN* 1.3 61.4 + - - +
75D MET* 3.4 25.4 + - + +
76D ASP* 3.2 23.7 + - - +
80D THR* 3.6 19.5 + - + +
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Residues in contact with ASN 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D GLU* 4.8 8.0 - - - +
54D PHE 5.1 1.2 + - - -
69D GLN 2.9 18.5 + - - +
70D THR* 3.4 7.7 - - - +
72D MET* 1.3 75.6 - - - +
74D SER* 1.3 61.3 + - - +
76D ASP 4.4 0.4 - - - -
77D PRO* 3.1 38.4 + - - +
80D THR* 2.8 31.1 + - - +
81D PRO* 3.4 5.3 - - - +
82D PRO* 3.2 37.8 - - + +
90E ARG* 2.8 29.1 + - - +
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Residues in contact with SER 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D PHE* 3.5 35.8 - - - -
70D THR 3.0 7.5 + - - -
71D LEU* 2.7 20.9 + - - -
73D ASN* 1.3 80.1 - - - +
75D MET* 1.3 57.9 + - - +
90E ARG* 4.8 5.2 - - - +
91E THR 4.4 3.4 - - - -
92E ILE* 3.0 35.5 - - - +
93E LEU* 3.0 29.3 + - - +
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Residues in contact with MET 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B ASP* 4.0 25.4 - - + +
31B MET* 3.9 31.9 - - + +
71D LEU* 3.3 17.2 + - - +
72D MET* 3.7 28.7 - - + +
73D ASN 3.3 0.2 - - - -
74D SER* 1.3 83.1 + - - +
76D ASP* 1.3 62.0 + - + +
77D PRO* 4.0 1.4 - - - +
92E ILE* 4.3 2.9 - - - +
93E LEU* 3.6 25.1 - - + +
95E ARG* 4.2 7.6 - - - +
131E VAL* 3.8 8.1 - - - +
151E LYS* 3.2 35.6 - - - +
153E LYS* 5.8 4.9 - - - +
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Residues in contact with ASP 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D MET 3.2 10.1 + - - +
73D ASN 3.5 2.2 - - - +
75D MET* 1.3 83.0 - - + +
77D PRO* 1.4 65.0 - - - +
78D GLU* 3.2 25.6 - - - +
79D SER* 2.8 36.3 + - - +
80D THR 3.3 10.4 + - - +
131E VAL* 3.3 23.2 - - + +
151E LYS* 5.3 2.2 - - - -
153E LYS* 6.0 3.5 + - - +
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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