Contacts of the helix formed by residues 69 - 80 (chain A) in PDB entry 4U2M
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 GLY 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A ALA 3.2 0.8 + - - -
68A ALA* 1.3 75.1 - - - +
70A LEU* 1.3 61.7 + - - +
71A GLY 3.3 2.7 - - - -
72A GLN* 3.4 8.7 + - - +
73A VAL* 3.2 24.8 + - - +
88A ASN* 6.0 2.2 - - - -
91A ASP* 3.7 26.9 - - - +
92A VAL* 4.2 10.9 - - - +
95A VAL* 4.1 10.1 - - - +
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Residues in contact with LEU 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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28A PHE* 3.7 41.3 - - + -
29A VAL 6.3 0.7 - - - -
35A PHE* 4.9 7.9 - - + -
49A PHE* 4.8 11.2 - - + -
66A ASN* 4.6 14.4 - - - +
67A ALA* 3.2 18.4 + - + +
68A ALA 3.3 0.6 - - - -
69A GLY* 1.3 76.8 - - - +
71A GLY* 1.3 67.8 + - - +
73A VAL* 3.1 7.6 + - + +
74A LEU* 2.9 42.3 + - + +
95A VAL* 4.1 20.5 - - + +
99A LEU* 4.8 10.5 - - + -
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Residues in contact with GLY 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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18A ARG* 5.4 0.7 + - - -
35A PHE* 3.7 39.1 - - - -
68A ALA 4.5 3.6 + - - -
69A GLY* 3.3 0.8 - - - -
70A LEU* 1.3 78.2 - - - +
72A GLN* 1.3 62.2 + - - +
74A LEU* 3.4 2.8 + - - +
75A GLU* 3.0 24.4 + - - +
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Residues in contact with GLN 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 ALA 5.6 0.2 + - - -
69A GLY* 3.4 10.8 + - - +
70A LEU 3.1 0.4 - - - -
71A GLY* 1.3 78.3 + - - +
73A VAL* 1.3 62.5 + - - +
75A GLU* 3.4 15.8 + - - +
76A PHE* 3.0 22.7 + - - +
81A LYS 4.4 0.9 - - - +
82A LEU* 4.0 11.1 - - + +
83A SER* 3.1 53.9 + - - +
88A ASN* 3.7 15.6 - - - +
92A VAL* 3.8 15.9 - - + -
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Residues in contact with VAL 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLY 3.2 13.2 + - - +
70A LEU* 3.1 11.5 + - + +
72A GLN* 1.3 77.0 - - - +
74A LEU* 1.3 62.8 + - + +
76A PHE* 3.2 4.4 + - - +
77A MET* 3.0 31.3 + - + +
82A LEU* 5.1 0.4 - - - -
92A VAL* 4.5 14.8 - - + +
95A VAL* 3.7 22.9 - - + -
96A ALA* 4.7 3.8 - - - +
99A LEU* 4.1 10.1 - - + -
101A MET* 3.6 33.0 - - + -
104A ILE* 4.0 17.0 - - + -
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Residues in contact with LEU 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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18A ARG* 4.1 14.4 - - - +
28A PHE* 4.2 21.1 - - + -
35A PHE* 3.6 39.5 - - + -
36A LYS 5.2 0.7 - - - +
37A ALA* 4.6 7.4 - - + -
42A LEU* 3.9 31.2 - - + -
49A PHE* 5.5 1.6 - - + -
70A LEU* 2.9 32.8 + - + +
71A GLY* 3.8 4.5 - - - +
73A VAL* 1.3 76.5 - - + +
75A GLU* 1.3 64.4 + - - +
77A MET* 3.1 19.8 + - + +
78A TYR* 3.1 24.2 + - + -
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Residues in contact with GLU 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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15A ASN* 5.3 0.7 + - - -
18A ARG* 3.0 30.2 + - - +
71A GLY 3.0 18.4 + - - +
72A GLN* 3.5 20.4 - - - +
74A LEU* 1.3 76.6 - - - +
76A PHE* 1.3 58.2 + - - +
78A TYR 3.3 0.5 + - - -
79A THR* 2.7 56.6 + - - +
81A LYS* 4.4 6.7 - - + +
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Residues in contact with PHE 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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45A CYS* 5.6 0.4 - - + -
72A GLN 3.0 13.2 + - - +
73A VAL 3.5 6.5 - - - +
74A LEU 3.2 0.2 - - - -
75A GLU* 1.3 77.9 - - - +
77A MET* 1.3 67.7 + - - +
80A ALA* 2.8 32.2 + - - -
81A LYS 3.3 17.6 + - - +
82A LEU* 4.0 15.7 - - + -
101A MET* 3.7 22.4 - - + -
103A ASP* 4.4 20.6 - - + -
104A ILE* 3.5 23.1 - - + -
134A PHE* 3.5 34.5 - + + -
137A HIS* 3.4 37.2 + + + -
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Residues in contact with MET 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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11A LEU* 3.5 10.2 - - - +
41A VAL* 4.8 4.1 - - + +
42A LEU* 3.6 29.6 - - - +
45A CYS* 3.8 33.8 - - + -
46A SER* 4.3 2.2 - - - -
49A PHE* 4.2 26.2 - - + -
73A VAL* 3.0 24.9 + - + +
74A LEU* 3.1 16.6 + - + +
76A PHE* 1.3 79.3 - - - +
78A TYR* 1.3 66.3 + - + +
101A MET* 3.6 37.5 - - + -
137A HIS* 2.8 24.6 + - - -
141A VAL* 4.3 1.0 - - - +
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Residues in contact with TYR 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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11A LEU* 3.4 21.8 - - + +
12A GLU* 5.3 0.3 - - - -
14A LEU* 3.5 41.3 - - + -
15A ASN* 3.5 34.4 - - - +
18A ARG* 3.5 35.0 - - + +
37A ALA* 3.6 4.8 - - + +
38A HIS* 2.7 49.3 + - - +
41A VAL* 3.6 24.7 - - + +
42A LEU* 4.3 14.4 - - + -
74A LEU* 3.1 23.8 + - + +
75A GLU 4.2 0.2 - - - +
77A MET* 1.3 82.1 - - + +
79A THR* 1.3 59.2 + - - +
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Residues in contact with THR 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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8A GLN* 5.5 3.5 + - - -
11A LEU* 4.1 7.4 - - - +
15A ASN* 3.6 24.0 - - - +
75A GLU* 2.7 45.0 + - - +
78A TYR* 1.3 79.8 - - + +
80A ALA* 1.3 65.7 + - - +
81A LYS* 3.0 41.6 + - - +
133A GLN* 5.6 0.3 - - - +
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Residues in contact with ALA 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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8A GLN* 5.6 3.6 - - - +
11A LEU* 4.4 6.5 - - + -
76A PHE* 2.8 21.6 + - - -
79A THR* 1.3 78.0 - - - +
81A LYS* 1.3 59.0 + - - +
132A ILE 3.5 1.4 - - - +
133A GLN* 3.5 5.8 - - + -
134A PHE* 2.9 49.3 + - - +
137A HIS* 3.7 24.4 - - + -
138A ALA 5.0 1.1 - - - +
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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