Contacts of the helix formed by residues 71 - 80 (chain A) in PDB entry 1ZN7
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A ILE* 3.6 25.8 - - + -
32A VAL* 4.7 2.7 - - + -
33A LEU* 3.6 22.7 - - + -
39A PHE* 3.7 28.0 - + - -
42A ALA* 4.9 2.9 - - + -
43A ILE* 3.8 18.9 - - + +
46A LEU* 5.2 1.8 - - + -
67A ARG 3.5 15.5 - - - -
68A GLY* 3.1 5.9 + - - +
70A LEU* 1.3 83.8 - - + +
72A GLY* 1.3 58.6 + - - +
73A PRO* 3.5 1.1 - - - -
74A SER 3.5 2.6 + - - -
75A LEU* 3.0 31.1 + - - +
126A VAL* 4.0 17.7 - - + -
127A ASP 4.9 0.2 - - - -
128A ASP* 3.8 12.6 - - + -
156A LEU* 3.5 47.3 - - + -
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Residues in contact with GLY 72 (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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61A ILE* 4.0 3.2 - - - +
63A GLY* 4.6 2.0 - - - -
68A GLY 2.9 13.0 + - - -
71A PHE* 1.3 75.5 - - - +
73A PRO* 1.3 62.3 - - - +
75A LEU* 3.8 1.0 - - - +
76A ALA* 2.8 31.5 + - - +
83A CYS* 3.6 17.8 - - - -
126A VAL* 3.6 21.4 - - - +
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Residues in contact with PRO 73 (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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69A PHE* 3.1 22.2 - - - +
70A LEU 4.8 0.9 - - - -
71A PHE 3.8 2.0 - - - +
72A GLY* 1.3 84.3 - - - +
74A SER* 1.3 55.8 + - - +
76A ALA* 3.4 2.1 + - + +
77A GLN* 2.8 36.8 + - - +
83A CYS* 4.1 13.5 - - + -
33B LEU* 3.5 22.0 - - + -
39B PHE* 3.6 27.6 - - + -
70B LEU* 3.5 29.8 - - + +
74B SER* 4.3 2.7 - - - +
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Residues in contact with SER 74 (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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39A PHE* 3.4 39.1 - - - -
43A ILE* 3.6 10.9 - - - +
70A LEU 4.7 1.2 + - - -
71A PHE 3.5 5.9 + - - -
72A GLY 3.4 0.4 - - - -
73A PRO* 1.3 74.8 - - - +
75A LEU* 1.3 60.8 + - - +
77A GLN* 3.5 6.1 + - - +
78A GLU* 2.9 29.1 + - - +
73B PRO* 4.3 1.7 - - - +
74B SER* 3.0 28.4 + - - -
77B GLN* 5.1 0.9 - - - +
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Residues in contact with LEU 75 (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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43A ILE* 4.0 15.5 - - + +
46A LEU* 3.9 17.3 - - + -
47A ALA* 3.6 40.4 - - + +
50A LEU* 3.9 17.7 - - + -
61A ILE* 4.2 11.2 - - + -
71A PHE* 3.0 18.9 + - + +
72A GLY 3.8 3.1 - - - +
74A SER* 1.3 72.1 - - - +
76A ALA* 1.3 67.7 + - - +
78A GLU* 3.2 2.3 + - - +
79A LEU* 3.1 39.6 + - + +
124A VAL* 5.4 0.2 - - + -
126A VAL* 4.2 28.0 - - + -
154A VAL* 4.4 3.6 - - + -
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Residues in contact with ALA 76 (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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61A ILE* 3.7 15.8 - - + +
72A GLY 2.8 21.4 + - - +
73A PRO* 3.6 4.3 - - + +
75A LEU* 1.3 71.5 - - - +
77A GLN* 1.3 61.5 + - + +
79A LEU* 3.0 4.0 + - - -
80A GLY 3.0 4.9 + - - -
81A LEU* 2.8 45.0 + - - +
82A GLY 3.6 21.5 - - - +
83A CYS* 3.8 8.7 - - + -
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Residues in contact with GLN 77 (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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73A PRO 2.8 24.6 + - - +
74A SER* 3.7 7.4 - - - +
76A ALA* 1.3 71.6 - - + +
78A GLU* 1.3 63.0 + - - +
80A GLY* 3.1 13.7 + - - +
81A LEU 3.8 2.5 + - - +
36B PRO* 2.9 44.2 + - - +
39B PHE* 3.4 33.5 - - + +
40B ARG* 3.1 39.1 + - - +
74B SER* 5.2 0.9 - - - +
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Residues in contact with GLU 78 (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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43A ILE* 3.9 17.4 - - + +
44A GLY* 5.1 7.2 - - - -
47A ALA* 3.5 25.2 - - + +
51A LYS* 4.7 15.2 + - - +
74A SER 2.9 18.2 + - - +
75A LEU 3.2 5.1 + - - +
77A GLN* 1.3 76.2 - - - +
79A LEU* 1.3 60.4 + - - +
80A GLY 3.7 0.2 + - - -
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Residues in contact with LEU 79 (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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47A ALA* 3.7 22.7 - - + +
50A LEU* 4.0 11.2 - - + -
51A LYS* 3.5 40.4 - - + +
58A ILE* 4.5 9.2 - - + -
61A ILE* 3.8 27.1 - - + -
75A LEU* 3.1 29.3 + - + +
76A ALA 3.0 5.0 + - - +
78A GLU* 1.3 77.8 - - - +
80A GLY* 1.3 59.1 + - - +
81A LEU* 3.6 23.2 + - + +
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Residues in contact with GLY 80 (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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76A ALA 3.0 2.0 + - - -
77A GLN* 3.1 12.6 + - - -
78A GLU 3.4 1.4 + - - -
79A LEU* 1.3 78.3 - - - +
81A LEU* 1.3 63.8 + - - +
36B PRO* 3.9 18.6 - - - +
40B ARG* 5.5 4.3 - - - -
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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