Contacts of the helix formed by residues 60 - 71 (chain B) in PDB entry 3ZO7
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 60 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 3.6 21.5 - - - -
3B TYR* 3.4 8.4 + - - -
58B VAL* 3.4 9.6 + - - +
59B ASN* 1.3 81.4 - - - +
61B HIS* 1.3 64.2 + - - +
62B ASP* 3.7 9.4 + - - +
63B GLU* 3.1 28.4 + - - +
64B LEU* 3.1 17.3 + - - +
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Residues in contact with HIS 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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1A MET* 3.7 23.3 - - + +
2A LEU 3.0 29.2 + - - -
3A TYR* 3.3 40.8 - + - -
61A HIS* 3.8 4.3 - + - -
83A PRO* 3.4 23.1 - - + +
84A LEU 3.2 21.8 - - - +
85A SER* 3.4 12.8 + - - +
3B TYR* 2.9 29.1 + - - -
60B SER* 1.3 69.9 - - - +
62B ASP* 1.3 62.3 + - - +
64B LEU* 3.1 4.9 + - - +
65B HIS* 2.9 26.2 + - - +
47D THR* 3.6 10.7 - - - +
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Residues in contact with ASP 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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85A SER* 3.2 11.7 - - - -
86A HIS* 2.7 44.4 + - - +
60B SER* 3.3 9.2 + - - +
61B HIS* 1.3 78.7 - - - +
63B GLU* 1.3 62.2 + - - +
65B HIS* 3.4 2.9 + - - +
66B GLU* 3.2 31.1 + - + +
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Residues in contact with GLU 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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39B GLN* 3.9 15.0 - - - +
58B VAL* 3.6 13.3 - - + +
59B ASN* 3.2 39.3 + - - +
60B SER* 3.1 23.3 + - - +
61B HIS 3.1 0.2 - - - -
62B ASP* 1.3 77.1 - - - +
64B LEU* 1.3 64.2 + - - +
66B GLU* 3.5 4.8 + - - +
67B ILE* 3.2 36.4 + - + +
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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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3B TYR* 3.4 37.7 - - + -
5B VAL* 4.6 1.8 - - + -
56B PHE* 3.9 38.6 - - + -
58B VAL* 3.8 19.0 - - + +
60B SER 3.1 8.2 + - - +
61B HIS* 3.1 8.0 + - - +
63B GLU* 1.3 74.1 - - - +
65B HIS* 1.3 67.6 + - - +
67B ILE* 3.2 6.9 + - + +
68B LEU* 2.9 45.6 + - + +
81B VAL* 3.8 18.2 - - + -
47D THR* 4.2 8.5 - - + -
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Residues in contact with HIS 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A SER* 3.8 12.1 - - - +
86A HIS 5.9 1.6 - - - -
88A PRO* 6.2 0.4 - - - +
61B HIS 2.9 16.9 + - - +
62B ASP* 3.6 5.2 - - - +
64B LEU* 1.3 77.2 - - - +
66B GLU* 1.3 78.4 + - - +
68B LEU* 3.3 3.0 + - - +
69B TRP* 2.8 58.5 + + + +
45D ARG* 3.3 47.4 + - + +
46D THR 4.0 0.2 + - - -
47D THR* 4.0 8.0 - - + +
48D GLY* 3.4 22.8 + - - +
49D LYS 3.6 12.8 - - - -
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Residues in contact with GLU 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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88A PRO* 6.0 2.4 - - - +
62B ASP* 3.2 17.7 + - + +
63B GLU* 4.0 4.9 - - - +
65B HIS* 1.3 91.0 - - - +
67B ILE* 1.3 63.0 + - + +
69B TRP* 3.5 14.3 + - - +
70B SER* 3.1 24.8 + - - -
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Residues in contact with ILE 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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30B ARG* 4.7 6.1 - - - +
34B LEU* 3.9 31.4 - - + -
39B GLN* 3.6 33.4 - - + +
56B PHE* 4.1 20.2 - - + -
58B VAL* 3.9 22.7 - - + -
63B GLU* 3.2 20.1 + - + +
64B LEU* 3.2 8.7 + - - +
66B GLU* 1.3 77.0 - - + +
68B LEU* 1.3 64.4 + - + +
70B SER* 2.8 24.0 + - - -
71B LEU* 3.4 12.1 + - + +
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Residues in contact with LEU 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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5B VAL* 4.4 7.9 - - + -
7B MET* 4.2 9.0 - - + -
56B PHE* 4.2 21.5 - - + -
64B LEU* 2.9 40.6 + - + +
65B HIS 3.7 3.1 - - - +
67B ILE* 1.3 75.9 - - - +
69B TRP* 1.3 63.0 + - - +
70B SER 3.1 1.0 + - - -
71B LEU* 3.1 37.0 + - + +
74B PHE* 3.0 23.0 - - + -
79B ILE* 4.3 13.2 - - + -
81B VAL* 4.0 15.7 - - + -
48D GLY* 3.7 28.7 - - - -
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Residues in contact with TRP 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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65B HIS* 2.8 44.2 + + + +
66B GLU* 3.7 18.4 - - - +
67B ILE 3.2 0.2 - - - -
68B LEU* 1.3 77.2 - - - +
70B SER* 1.3 61.2 + - - +
71B LEU 3.6 1.2 + - - +
74B PHE* 3.6 52.9 - + - +
24D LYS* 6.0 2.7 - - - -
45D ARG* 5.0 8.1 - - - -
49D LYS 4.0 4.9 - - - -
50D TYR* 3.7 55.0 - + - -
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Residues in contact with SER 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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30B ARG* 3.3 31.3 + - - +
66B GLU 3.1 12.6 + - - -
67B ILE 2.8 17.0 + - - -
68B LEU 3.1 0.4 - - - -
69B TRP* 1.3 77.7 - - - +
71B LEU* 1.3 65.2 + - - +
72B PRO* 3.4 8.0 - - - +
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Residues in contact with LEU 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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7B MET* 3.9 26.2 - - + -
30B ARG* 4.2 10.3 - - + -
34B LEU* 4.1 15.9 - - + -
40B TRP* 4.0 25.1 - - + -
56B PHE* 5.1 0.2 - - + -
67B ILE* 3.4 14.5 + - + +
68B LEU* 3.1 39.5 + - + +
69B TRP 4.2 0.7 - - - +
70B SER* 1.3 78.7 - - - +
72B PRO* 1.3 67.2 - - + +
73B PHE* 4.4 2.7 - - + +
74B PHE* 2.9 32.8 + - + +
75B PRO* 4.1 1.4 - - - +
77B LEU* 4.6 7.4 - - + -
79B ILE* 5.7 0.4 - - + -
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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