Contacts of the helix formed by residues 64 - 75 (chain B) in PDB entry 4Z2C
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 64 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B LYS 3.6 0.4 + - - -
63B LYS* 1.3 73.7 - - - +
65B ALA* 1.3 54.1 + - - +
67B ILE* 3.3 12.1 + - - +
68B THR* 2.7 37.9 + - - -
84B TYR* 3.5 29.4 - - - -
87B MET* 4.5 7.9 - - - +
107B PHE* 4.4 4.7 - - - -
118B GLN* 3.7 8.0 + - - -
121B THR* 2.7 41.1 + - - -
122B GLU* 4.0 5.5 + - - -
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Residues in contact with ALA 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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69A GLY* 3.6 10.6 - - - -
72A MET* 3.6 44.4 - - + -
80A ASP* 4.5 4.4 - - - +
63B LYS* 3.2 2.4 - - + -
64B SER* 1.3 75.8 - - - +
66B ARG* 1.3 60.4 + - - +
68B THR* 4.1 0.6 - - - -
69B GLY* 2.9 26.2 + - - -
118B GLN* 3.5 31.6 + - + +
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Residues in contact with ARG 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ARG* 6.1 0.4 - - - +
69A GLY* 3.8 18.4 + - - +
70A ASP* 3.9 21.6 + - - -
73A GLY* 3.9 16.5 - - - -
74A LYS* 3.3 40.6 - - - +
151A GLU* 4.7 4.8 + - - -
53B LEU* 3.4 28.9 - - + +
62B LYS* 4.7 9.3 - - + +
63B LYS* 3.1 19.4 + - - +
65B ALA* 1.3 79.0 - - - +
67B ILE* 1.3 58.6 + - + +
69B GLY* 3.7 0.5 - - - -
70B ASP* 2.9 51.1 + - - +
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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
----------------------------------------------------------
49B GLY 5.2 1.8 - - - +
50B MET* 3.7 37.9 - - + -
53B LEU* 5.1 9.2 - - + -
55B VAL* 5.0 4.9 - - + -
62B LYS* 3.7 16.4 - - + +
63B LYS 3.5 10.8 - - - +
64B SER* 3.3 6.0 + - - +
66B ARG* 1.3 74.5 - - + +
68B THR* 1.3 60.3 + - - +
70B ASP* 3.4 4.6 + - - +
71B VAL* 2.9 45.4 + - + +
87B MET* 3.5 26.0 - - + -
123B ALA* 3.4 33.7 - - + +
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Residues in contact with THR 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B SER 2.7 22.5 + - - -
65B ALA 4.1 2.7 - - - -
67B ILE* 1.3 76.5 - - - +
69B GLY* 1.3 58.0 + - - +
71B VAL* 3.8 0.9 - - - +
72B MET* 2.9 30.4 + - + +
80B ASP* 3.6 36.3 - - - +
83B ILE* 4.1 23.2 - - + +
84B TYR* 4.3 11.4 + - - +
87B MET* 5.1 4.1 - - - +
118B GLN* 3.4 30.7 + - - +
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Residues in contact with GLY 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ALA* 3.6 26.2 - - - -
66A ARG* 3.2 16.4 + - - +
69A GLY* 4.7 2.0 - - - -
65B ALA 2.9 19.7 + - - -
66B ARG 3.7 0.9 - - - -
68B THR* 1.3 79.1 - - - +
70B ASP* 1.3 56.2 + - - +
72B MET* 3.9 1.6 - - - +
73B GLY 2.9 25.5 + - - -
80B ASP* 5.1 2.2 + - - -
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Residues in contact with ASP 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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66A ARG* 3.5 30.1 + - - +
69A GLY 5.8 0.2 - - - -
70A ASP* 3.4 18.4 - - - +
49B GLY* 5.6 0.4 - - - +
53B LEU* 3.4 36.0 - - + +
66B ARG* 2.9 37.0 + - - +
67B ILE 3.8 3.1 - - - +
69B GLY* 1.3 73.0 - - - +
71B VAL* 1.3 59.3 + - + +
74B LYS* 2.9 48.5 + - - +
75B TYR* 5.0 0.2 - - - -
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Residues in contact with VAL 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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42B VAL 5.4 0.2 - - - +
45B ARG* 3.8 32.1 - - + +
46B ILE* 4.2 12.8 - - + -
49B GLY* 4.1 15.9 - - - -
67B ILE* 2.9 32.0 + - + +
68B THR 3.9 2.9 - - - +
70B ASP* 1.3 76.0 - - + +
72B MET* 1.3 58.1 + - - +
75B TYR* 2.9 17.4 + - + -
76B HIS* 2.8 43.2 + - + -
83B ILE* 4.0 21.1 - - + -
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Residues in contact with MET 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LYS* 5.1 6.1 - - + -
65A ALA* 3.5 22.9 - - + -
118A GLN 4.7 0.4 - - - +
119A ARG* 3.7 22.4 - - + -
68B THR 2.9 16.1 + - - +
69B GLY* 3.9 2.9 - - - +
71B VAL* 1.3 76.9 - - - +
73B GLY* 1.3 61.7 + - - +
74B LYS 3.3 0.7 + - - -
76B HIS 3.1 24.2 - - - +
77B PRO* 4.4 1.9 - - + +
78B HIS 3.2 29.8 - - - +
79B GLY* 3.6 3.1 - - - +
80B ASP* 3.3 50.0 - - - +
83B ILE* 3.9 5.8 - - + -
147B TYR* 3.0 18.2 + - - +
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Residues in contact with GLY 73 (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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63A LYS* 4.0 19.3 - - - +
65A ALA* 5.7 0.6 - - - +
66A ARG* 3.7 15.9 - - - -
69B GLY 2.9 17.4 + - - -
72B MET* 1.3 77.3 - - - +
74B LYS* 1.3 60.7 + - - +
146B ASN* 4.8 1.7 + - - -
147B TYR* 2.9 17.8 + - - -
148B ASP* 4.4 5.2 - - - +
150B ASN* 5.6 0.5 - - - +
151B GLU* 5.6 0.2 - - - +
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Residues in contact with LYS 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ARG* 4.1 22.2 - - - +
52B GLU* 4.3 9.7 - - - +
53B LEU* 3.9 15.0 - - - +
70B ASP* 2.9 42.5 + - - +
73B GLY* 1.3 81.5 - - - +
75B TYR* 1.3 102.4 + - + +
146B ASN* 2.6 35.2 + - - +
147B TYR* 3.7 2.3 - - - -
151B GLU* 3.8 29.2 - - + +
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Residues in contact with TYR 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ARG* 3.2 44.1 + - + -
48B TYR* 3.6 32.4 - + - -
49B GLY* 3.8 19.5 - - - -
52B GLU* 3.6 10.4 - - - +
70B ASP 4.5 0.9 - - - -
71B VAL* 2.9 24.1 + - - +
73B GLY 3.9 0.4 - - - -
74B LYS* 1.3 124.7 + - + +
76B HIS* 1.3 59.0 + - - +
77B PRO* 3.1 13.4 - - - +
146B ASN* 4.6 2.7 - - + -
147B TYR* 3.3 12.3 + - - +
151B GLU* 4.6 10.6 + - + -
152B ARG 3.9 9.4 - - - -
153B GLU* 3.6 25.8 - - + +
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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