Contacts of the helix formed by residues 64 - 75 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A LYS 3.4 1.8 + - - -
63A LYS* 1.3 72.7 - - - +
65A ALA* 1.3 59.6 + - - +
67A ILE* 3.2 14.8 + - - +
68A THR* 2.9 34.2 + - - +
84A TYR* 3.6 22.9 - - - -
87A MET* 4.8 7.6 - - - -
107A PHE* 5.7 0.7 - - - -
118A GLN* 3.9 5.6 - - - -
121A THR* 2.9 37.5 + - - -
122A GLU* 4.7 2.9 - - - -
123A ALA* 5.4 0.4 - - - -
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Residues in contact with ALA 65 (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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63A LYS* 3.2 2.9 - - + -
64A SER* 1.3 77.7 - - - +
66A ARG* 1.3 55.8 + - - +
68A THR* 3.1 9.4 + - - -
69A GLY* 2.9 24.9 + - - -
80A ASP* 5.4 0.9 - - - +
118A GLN* 3.5 22.4 + - + +
69B GLY* 3.6 14.1 - - - +
72B MET* 3.5 37.0 - - + -
73B GLY 5.7 0.2 - - - +
80B ASP* 4.5 8.3 - - - +
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Residues in contact with ARG 66 (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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53A LEU* 3.9 30.2 - - + +
62A LYS* 5.2 11.1 - - + +
63A LYS* 3.0 17.3 + - + +
65A ALA* 1.3 77.0 - - - +
67A ILE* 1.3 60.3 + - + +
69A GLY* 3.3 1.0 + - - -
70A ASP* 2.9 41.6 + - - +
66B ARG* 6.1 0.2 - - - +
69B GLY 3.2 22.4 + - - +
70B ASP* 3.5 37.6 + - - +
73B GLY* 3.7 17.1 - - - -
74B LYS* 4.1 26.2 - - - +
151B GLU* 4.4 7.3 + - - -
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Residues in contact with ILE 67 (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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46A ILE* 4.9 1.1 - - + +
49A GLY 5.4 0.9 - - - -
50A MET* 3.7 34.1 - - + +
53A LEU* 4.8 10.7 - - + +
55A VAL* 5.0 6.3 - - + -
62A LYS* 3.4 31.6 - - + +
63A LYS 3.6 7.9 - - - +
64A SER* 3.2 10.3 + - - +
66A ARG* 1.3 77.2 - - + +
68A THR* 1.3 56.4 + - - +
70A ASP* 3.3 5.1 + - - +
71A VAL* 2.9 42.5 + - + +
87A MET* 3.6 18.8 - - + -
123A ALA* 3.7 30.5 - - + +
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Residues in contact with THR 68 (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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64A SER 2.9 15.6 + - - +
65A ALA* 3.1 9.4 + - - -
67A ILE* 1.3 72.8 - - - +
69A GLY* 1.3 62.5 + - - +
71A VAL* 4.0 0.5 - - - +
72A MET* 2.9 32.4 + - - +
80A ASP* 2.9 20.2 + - - +
83A ILE* 4.0 16.6 - - + +
84A TYR* 3.8 24.9 - - + +
87A MET* 3.6 21.5 - - + -
118A GLN* 2.9 24.8 + - - +
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Residues in contact with GLY 69 (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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65A ALA 2.9 20.5 + - - -
66A ARG 3.3 1.7 + - - -
68A THR* 1.3 77.1 + - - +
70A ASP* 1.3 57.2 + - - +
72A MET* 3.9 4.0 - - - +
73A GLY* 2.9 26.2 + - - -
80A ASP* 5.2 2.9 - - - -
65B ALA* 3.6 23.8 - - - -
66B ARG* 3.8 13.3 + - - +
69B GLY* 4.7 2.2 - - - -
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Residues in contact with ASP 70 (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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49A GLY* 5.5 0.7 - - - +
53A LEU* 3.2 37.7 - - + +
66A ARG* 2.9 19.9 + - - +
67A ILE 3.7 2.0 - - - +
69A GLY* 1.3 75.0 - - - +
71A VAL* 1.3 61.2 + - + +
74A LYS* 2.9 54.4 + - - +
75A TYR* 4.8 2.0 - - + -
66B ARG* 3.9 23.1 + - - +
70B ASP* 3.4 23.4 - - - +
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Residues in contact with VAL 71 (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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42A VAL 5.1 0.2 - - - +
45A ARG* 3.6 33.4 - - + +
46A ILE* 3.9 17.3 - - + -
49A GLY* 4.3 11.0 - - - -
67A ILE* 2.9 30.0 + - + +
68A THR 4.0 3.6 - - - +
70A ASP* 1.3 75.4 - - + +
72A MET* 1.3 52.5 - - - +
75A TYR* 2.9 17.0 + - - -
76A HIS* 2.6 43.1 + - + -
83A ILE* 3.7 27.8 - - + -
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Residues in contact with MET 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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68A THR 2.9 19.3 + - - +
69A GLY 3.9 1.6 - - - +
71A VAL* 1.3 79.9 - - - +
73A GLY* 1.3 63.0 + - - +
74A LYS 3.4 0.2 + - - -
76A HIS 3.2 22.3 - - - +
77A PRO* 4.5 1.8 - - - +
78A HIS 3.1 20.9 - - - +
80A ASP* 3.5 42.0 - - + +
83A ILE* 3.7 8.5 - - + +
147A TYR* 2.8 20.6 + - - +
63B LYS* 5.5 4.0 - - + -
65B ALA* 3.6 30.7 - - + -
118B GLN* 5.2 1.3 - - + -
119B ARG* 3.5 29.8 - - + +
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Residues in contact with GLY 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 GLY 2.9 17.5 + - - -
70A ASP 3.4 0.2 + - - -
72A MET* 1.3 81.5 - - - +
74A LYS* 1.3 61.3 + - - +
146A ASN* 4.8 2.6 + - - -
147A TYR* 2.9 17.2 + - - -
148A ASP* 5.3 3.5 - - - +
150A ASN* 5.7 0.2 - - - +
63B LYS* 4.6 15.5 - - - +
66B ARG* 3.9 17.3 - - - -
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Residues in contact with LYS 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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49A GLY 5.9 0.4 - - - -
52A GLU* 4.2 16.2 + - - +
53A LEU* 5.6 1.9 - - - +
70A ASP* 2.9 35.6 + - - +
73A GLY* 1.3 81.7 - - - +
75A TYR* 1.3 100.3 + - + +
146A ASN* 3.0 31.5 + - - +
147A TYR* 3.9 2.7 - - - -
151A GLU* 3.7 34.3 + - + +
66B ARG* 3.3 31.0 - - - +
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Residues in contact with TYR 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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45A ARG* 3.3 46.3 + - + -
48A TYR* 3.4 33.9 + + - -
49A GLY* 3.8 19.3 - - - -
52A GLU* 3.6 9.0 - - - +
70A ASP 4.4 1.8 - - - -
71A VAL* 2.9 20.2 + - - +
73A GLY 3.8 0.4 - - - -
74A LYS* 1.3 130.3 + - + +
76A HIS* 1.3 58.3 + - - +
77A PRO* 3.2 12.9 - - - +
146A ASN* 4.8 3.0 - - + +
147A TYR* 3.5 11.5 + - - -
151A GLU* 4.7 9.1 + - + -
152A ARG 3.7 12.3 + - - -
153A GLU* 4.0 22.1 - - + +
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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