Contacts of the helix formed by residues 52 - 72 (chain B) in PDB entry 4ZPK
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 52 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35B TYR* 4.9 0.9 - - - -
51B LEU* 1.3 83.9 - - + +
53B LYS* 1.3 65.7 + - - +
54B ALA* 2.8 29.8 + - - +
55B SER* 3.0 27.0 + - - +
56B ILE* 3.1 20.6 + - - +
9D G 3.4 36.3 + - - +
10D C 3.7 9.0 + - - -
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Residues in contact with LYS 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A MET* 3.4 24.6 - - + +
30B GLU* 4.9 5.8 - - - +
34B PHE* 3.4 51.4 - - + -
35B TYR* 5.2 5.7 - - + -
51B LEU 3.7 0.8 + - - -
52B ASP* 1.3 80.2 - - - +
54B ALA* 1.3 59.9 + - - +
56B ILE* 3.2 19.8 - - - +
57B MET* 3.3 26.1 - - - +
10D C 3.0 36.1 + - - +
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Residues in contact with ALA 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LYS* 4.0 22.7 - - - +
105A MET* 3.1 31.0 - - + -
108A TYR* 4.2 6.5 - - + +
52B ASP* 2.8 10.7 + - - +
53B LYS* 1.3 74.9 - - + +
55B SER* 1.3 58.6 + - - +
57B MET* 2.8 26.0 + - - +
58B ARG* 3.0 15.4 + - + +
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Residues in contact with SER 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LEU* 4.1 14.4 - - - -
52B ASP* 3.0 29.0 + - - +
53B LYS 3.3 0.2 - - - -
54B ALA* 1.3 77.5 - - - +
56B ILE* 1.3 57.7 + - - +
58B ARG* 2.9 42.6 + - - +
59B LEU* 2.9 38.4 + - - +
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Residues in contact with ILE 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B PHE* 4.3 17.9 - - + +
35B TYR* 4.0 24.0 - - + -
37B LEU* 3.7 31.2 - - + -
38B ALA* 3.5 35.4 - - + +
41B LEU* 4.6 5.0 - - + +
51B LEU* 3.6 19.3 - - + +
52B ASP 3.1 19.3 - - - +
53B LYS* 3.2 12.6 - - - +
54B ALA 3.1 0.2 - - - -
55B SER* 1.3 78.7 - - - +
57B MET* 1.3 58.1 + - - +
59B LEU* 3.4 1.6 + - - +
60B ALA* 2.9 28.4 + - - +
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Residues in contact with MET 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A MET* 4.0 9.2 - - - -
108A TYR* 3.3 47.1 - - + +
109A ILE* 3.8 14.8 - - + +
112A LEU* 3.7 33.0 - - + -
132A LEU* 5.1 1.8 - - - -
34B PHE* 4.1 20.6 - - + -
37B LEU* 4.8 7.0 - - - -
53B LYS* 3.3 24.2 - - - +
54B ALA* 2.8 14.2 + - - +
56B ILE* 1.3 72.5 - - - +
58B ARG* 1.3 65.6 + - - +
60B ALA* 3.2 3.7 + - - +
61B ILE* 2.9 34.5 + - + +
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Residues in contact with ARG 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A TYR* 3.3 34.7 - - + +
54B ALA* 3.0 12.7 + - - +
55B SER* 2.9 39.2 + - - +
57B MET* 1.3 76.4 - - - +
59B LEU* 1.3 59.0 + - - +
61B ILE* 3.4 4.4 + - - +
62B SER* 2.5 38.7 + - - -
124B VAL 3.0 27.7 + - - -
125B GLU* 3.3 16.6 + - - +
126B LEU 3.9 1.4 - - - +
127B THR 3.6 16.8 + - - +
128B GLY* 4.3 8.0 - - - -
129B HIS* 3.1 46.3 + - - +
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Residues in contact with LEU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A PHE* 3.7 21.2 - - + -
41B LEU* 4.1 11.2 - - + -
43B LEU* 3.8 21.5 - - + -
51B LEU* 3.6 33.2 - - + -
55B SER* 2.9 20.5 + - - +
56B ILE 3.9 2.7 - - - +
58B ARG* 1.3 73.1 - - - +
60B ALA* 1.3 61.5 + - - +
62B SER* 3.7 4.2 - - - -
63B PHE* 2.9 33.5 + - - +
123B GLN 4.5 1.3 - - - +
124B VAL* 4.2 22.2 - - + +
127B THR* 3.6 34.1 - - - +
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Residues in contact with ALA 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A LEU* 5.0 9.0 - - + -
135A ALA* 6.5 0.2 - - + -
139A MET* 3.7 25.8 - - + -
37B LEU* 4.2 19.7 - - + -
41B LEU* 4.2 1.9 - - + +
56B ILE 2.9 17.9 + - - +
57B MET* 3.6 4.9 - - - +
59B LEU* 1.3 78.3 - - - +
61B ILE* 1.3 63.6 + - + +
63B PHE* 3.4 1.6 - - - +
64B LEU* 3.0 36.4 + - + +
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Residues in contact with ILE 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A TYR* 3.7 44.2 - - + +
111A GLU* 3.9 17.9 - - + +
112A LEU* 4.3 23.3 - - + +
115A MET* 4.8 4.0 - - + +
57B MET* 2.9 28.1 + - + +
58B ARG* 3.6 3.6 - - - +
60B ALA* 1.3 73.3 - - + +
62B SER* 1.3 63.4 + - - +
64B LEU* 3.3 9.6 + - - +
65B ARG* 2.9 62.5 + - + +
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Residues in contact with SER 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B ARG 2.5 23.5 + - - -
59B LEU 3.7 2.5 - - - -
61B ILE* 1.3 77.9 - - - +
63B PHE* 1.3 64.3 + - - +
65B ARG* 3.7 1.7 - - - +
66B THR* 2.8 29.8 + - - -
109B ILE* 3.4 34.1 - - - +
127B THR* 3.4 15.7 + - - -
128B GLY* 3.1 24.1 - - - -
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Residues in contact with PHE 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A MET* 3.4 33.4 - - + -
142A LEU* 3.4 40.2 - - + -
158A PHE* 3.9 30.1 - + + -
159A LEU* 5.8 0.9 - - + -
40B GLU* 4.9 4.9 - - - -
41B LEU* 5.1 1.1 - - + -
42B PRO* 3.9 33.9 - - + -
59B LEU 2.9 21.9 + - - +
60B ALA* 3.4 3.8 - - - +
62B SER* 1.3 72.1 - - - +
64B LEU* 1.3 63.6 + - + +
66B THR* 3.4 7.0 + - - -
67B HIS* 3.0 51.0 + + - +
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Residues in contact with LEU 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A LEU* 3.6 31.0 - - + -
115A MET* 4.0 20.8 - - + +
116A VAL* 4.5 10.1 - - + -
135A ALA* 6.1 0.4 - - + -
138A HIS* 4.2 25.6 - - + +
139A MET* 3.8 28.7 - - + -
142A LEU* 4.6 5.6 - - + -
60B ALA* 3.0 24.2 + - + +
61B ILE 3.6 3.8 - - - +
63B PHE* 1.3 86.0 - - + +
65B ARG* 1.3 57.3 + - - +
67B HIS* 3.3 7.0 + - - +
68B LYS* 2.9 25.9 + - - +
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Residues in contact with ARG 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A GLU* 2.5 43.9 + - - +
115A MET* 3.7 33.9 - - + +
61B ILE* 2.9 33.1 + - - +
62B SER 3.7 3.1 - - - +
64B LEU* 1.3 74.2 - - - +
66B THR* 1.3 67.0 + - - +
68B LYS* 2.9 19.6 + - + +
69B LEU* 2.9 17.3 + - - +
103B THR* 4.7 9.9 - - - +
107B ASP* 3.9 16.3 + - - +
109B ILE* 3.8 34.9 - - + +
128B GLY 5.9 0.2 + - - -
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Residues in contact with THR 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A PHE* 6.4 0.2 - - - -
159A LEU* 3.7 41.3 - - + -
167A LEU* 6.1 0.7 - - + -
62B SER 2.8 22.4 + - - -
63B PHE* 3.4 8.4 + - - -
65B ARG* 1.3 77.2 - - - +
67B HIS* 1.3 58.3 + - - +
69B LEU* 3.5 2.4 + - - +
70B LEU* 2.9 34.9 + - + +
101B VAL* 5.5 5.5 - - + +
109B ILE* 3.1 31.3 + - - +
110B PHE* 4.0 9.5 - - + +
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Residues in contact with HIS 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A LEU* 4.1 25.9 - - + +
158A PHE 4.3 2.0 - - - -
159A LEU* 3.8 18.4 - - + +
163A GLU* 3.3 28.3 + - - -
63B PHE* 3.0 41.4 + + - +
64B LEU* 3.6 9.9 - - - +
66B THR* 1.3 75.6 - - - +
68B LYS* 1.3 56.6 + - - +
70B LEU* 4.0 8.4 - - + +
71B SER* 2.9 33.1 + - - -
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Residues in contact with LYS 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A ASP 5.0 5.1 + - - -
115A MET* 4.0 32.3 - - + +
64B LEU 2.9 13.2 + - - +
65B ARG* 2.9 14.9 + - + +
67B HIS* 1.3 74.2 - - - +
69B LEU* 1.3 65.0 + - - +
71B SER* 2.9 18.2 + - - -
72B SER* 2.8 16.4 + - - -
202B TYR* 3.4 37.0 - - + -
203B ASN 5.1 2.6 + - - -
219B LEU* 5.3 13.1 - - + +
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Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A LEU* 6.2 1.6 - - + -
65B ARG 2.9 15.7 + - - +
66B THR* 4.2 3.1 - - - +
68B LYS* 1.3 75.1 - - - +
70B LEU* 1.3 63.5 + - - +
72B SER* 3.2 5.6 + - - -
73B VAL* 2.9 34.9 + - + +
101B VAL* 4.8 6.1 - - + -
200B ARG* 4.2 19.3 - - + +
201B VAL 4.0 5.4 - - - +
202B TYR* 3.7 36.6 - - + +
219B LEU* 6.1 2.0 - - + -
220B SER 4.9 2.2 - - - +
221B CYS* 3.5 41.5 - - + -
223B ILE* 4.6 9.9 - - + -
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Residues in contact with LEU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A LEU* 4.4 14.8 - - + -
163A GLU* 3.2 59.5 - - + +
166A HIS* 6.0 4.7 - - + +
167A LEU* 6.2 3.4 - - + -
66B THR* 2.9 21.6 + - + +
67B HIS* 3.7 9.0 - - + +
69B LEU* 1.3 78.9 - - - +
71B SER* 1.3 68.1 + - - +
73B VAL* 3.2 20.1 + - - +
74B CYS 4.0 4.3 - - - +
75B SER* 4.3 12.2 + - - +
76B GLU* 6.3 2.2 - - + -
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Residues in contact with SER 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B HIS 2.9 17.1 + - - -
68B LYS* 2.9 17.5 + - - -
70B LEU* 1.3 83.6 - - - +
72B SER* 1.3 57.6 + - - +
74B CYS* 2.8 28.6 + - - +
76B GLU* 4.8 9.6 - - - +
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Residues in contact with SER 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B LYS 2.8 21.4 + - - -
69B LEU 3.4 4.0 + - - -
71B SER* 1.3 76.4 + - - +
73B VAL* 1.3 55.2 + - - +
74B CYS* 2.9 10.6 + - - +
200B ARG* 5.8 0.3 - - - +
201B VAL 4.7 8.0 - - - +
202B TYR* 3.1 54.1 - - - +
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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