Contacts of the helix formed by residues 71 - 80 (chain B) in PDB entry 1ZN8
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 PHE 71 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ILE* 4.1 12.6 - - + -
32B VAL* 4.5 3.4 - - + -
33B LEU* 3.5 19.1 - - + -
39B PHE* 3.6 32.1 - + - -
42B ALA* 4.8 3.1 - - + -
43B ILE* 3.9 17.2 - - + +
46B LEU* 5.3 4.0 - - + -
67B ARG 3.5 19.5 - - - -
68B GLY* 3.1 6.2 + - - +
70B LEU* 1.3 84.4 - - + +
72B GLY* 1.3 67.1 + - - +
73B PRO 3.4 2.2 - - - -
74B SER 3.4 2.5 + - - -
75B LEU* 2.9 24.6 + - - +
126B VAL* 4.3 16.4 - - + -
127B ASP 5.1 0.2 - - - -
128B ASP* 4.0 18.8 - - + -
156B LEU* 3.7 46.4 - - + -
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Residues in contact with GLY 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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61B ILE* 3.9 8.5 - - - +
63B GLY* 4.8 1.1 - - - -
68B GLY 2.9 11.9 + - - -
71B PHE* 1.3 78.9 - - - +
73B PRO* 1.4 61.8 - - - +
75B LEU* 3.3 1.6 + - - +
76B ALA* 2.9 31.5 + - - +
83B CYS* 3.7 11.4 - - - -
126B VAL* 3.6 22.4 - - - +
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Residues in contact with PRO 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 3.6 24.9 - - + -
39A PHE* 3.6 26.2 - - + -
70A LEU* 3.6 21.1 - - + +
74A SER* 4.4 3.4 - - - +
69B PHE* 3.0 29.2 - - - +
70B LEU 4.6 0.9 - - - -
71B PHE 3.7 1.8 - - - +
72B GLY* 1.4 82.6 - - - +
74B SER* 1.3 56.1 + - - +
76B ALA* 3.6 1.7 - - + +
77B GLN* 2.8 35.3 + - - +
83B CYS* 4.2 14.8 - - + -
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Residues in contact with SER 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A PRO* 4.4 1.9 - - - +
74A SER* 3.1 26.0 + - - -
77A GLN* 5.4 0.7 - - - +
39B PHE* 3.5 25.2 - - - -
43B ILE* 3.7 26.1 - - - +
70B LEU 4.6 1.4 + - - -
71B PHE 3.4 3.3 + - - -
72B GLY 3.3 0.2 - - - -
73B PRO* 1.3 79.2 - - - +
75B LEU* 1.3 62.4 + - - +
77B GLN* 3.4 5.9 + - - +
78B GLU* 3.0 23.4 + - - +
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Residues in contact with LEU 75 (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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43B ILE* 3.9 14.9 - - + +
46B LEU* 3.8 19.5 - - + -
47B ALA* 3.6 39.0 - - + +
50B LEU* 4.0 16.8 - - + -
61B ILE* 4.4 10.5 - - + -
71B PHE* 2.9 18.5 + - + +
72B GLY 3.7 3.1 - - - +
74B SER* 1.3 71.8 - - - +
76B ALA* 1.3 66.8 + - - +
78B GLU* 3.3 2.9 + - - +
79B LEU* 3.1 38.8 + - + +
126B VAL* 4.3 28.9 - - + -
154B VAL* 4.5 3.4 - - + -
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Residues in contact with ALA 76 (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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61B ILE* 3.8 16.3 - - + +
72B GLY 2.9 18.6 + - - +
73B PRO 3.6 4.0 - - - +
75B LEU* 1.3 76.7 - - - +
77B GLN* 1.3 61.6 + - + +
79B LEU* 3.0 10.3 + - - +
81B LEU* 2.9 40.6 + - - +
82B GLY 3.5 22.0 - - - +
83B CYS* 3.9 6.5 - - + -
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Residues in contact with GLN 77 (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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36A PRO* 2.8 44.9 + - - +
39A PHE* 3.4 37.0 - - + +
40A ARG* 3.5 22.2 - - - +
74A SER* 5.4 0.9 - - - +
73B PRO 2.8 16.5 + - - +
74B SER* 3.7 6.7 - - - +
75B LEU 3.3 0.2 - - - -
76B ALA* 1.3 76.3 - - + +
78B GLU* 1.3 62.7 + - - +
80B GLY* 3.1 14.9 + - - +
81B LEU 4.3 2.7 + - - +
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Residues in contact with GLU 78 (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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43B ILE* 3.9 17.3 - - + +
44B GLY* 5.3 5.4 - - - -
47B ALA* 3.5 25.9 - - + +
51B LYS* 4.6 16.6 + - - +
74B SER 3.0 17.0 + - - +
75B LEU 3.6 5.4 - - - +
76B ALA 3.3 0.2 - - - -
77B GLN* 1.3 76.0 - - - +
79B LEU* 1.3 56.5 + - - +
80B GLY 3.4 0.9 + - - -
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Residues in contact with LEU 79 (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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47B ALA* 3.8 17.7 - - + +
50B LEU* 4.1 9.9 - - + -
51B LYS* 3.3 44.2 - - + +
58B ILE* 4.5 8.5 - - + -
61B ILE* 4.0 26.7 - - + -
75B LEU* 3.1 25.7 + - + +
76B ALA 3.0 7.2 + - - +
78B GLU* 1.3 75.7 - - - +
80B GLY* 1.3 61.3 - - - +
81B LEU* 3.5 27.1 - - + +
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Residues in contact with GLY 80 (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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36A PRO* 3.9 17.2 - - - +
76B ALA 3.1 2.2 + - - -
77B GLN* 3.1 14.3 + - - -
78B GLU 3.4 1.6 + - - -
79B LEU* 1.3 77.6 - - - +
81B LEU* 1.3 63.2 + - - +
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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