Contacts of the helix formed by residues 78 - 94 (chain A) in PDB entry 4CQM
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 GLU 78 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A ASP* 2.9 34.7 + - + +
77A SER* 1.3 87.9 + - - +
79A ALA* 1.3 60.5 + - - +
80A ARG* 4.4 3.1 - - + +
81A ALA* 3.7 15.3 - - + +
82A ALA* 2.9 32.1 + - - +
133A LEU* 3.6 1.6 - - - -
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Residues in contact with ALA 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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77A SER 3.8 0.8 + - - -
78A GLU* 1.3 72.7 + - - +
80A ARG* 1.3 62.1 + - - +
82A ALA* 3.9 1.4 - - - +
83A ARG* 3.2 25.6 + - - +
133A LEU* 3.5 28.1 - - + +
117D GLU* 3.3 38.4 + - + +
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Residues in contact with ARG 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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78A GLU* 3.3 3.3 - - + +
79A ALA* 1.3 80.4 - - - +
81A ALA* 1.3 62.5 + - - +
83A ARG* 4.2 22.1 - - - +
84A CYS* 3.3 26.7 + - + +
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Residues in contact with ALA 81 (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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74A ALA* 3.8 10.9 - - + +
75A ASP* 3.4 34.5 - - + +
78A GLU* 3.4 15.1 + - + +
80A ARG* 1.3 78.3 - - - +
82A ALA* 1.3 62.6 + - - +
84A CYS* 4.2 3.5 - - - +
85A LEU* 3.2 22.2 + - - +
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Residues in contact with ALA 82 (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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74A ALA* 5.4 0.4 - - - -
75A ASP 4.3 1.7 + - - -
76A VAL* 4.1 12.1 - - - +
78A GLU 2.9 18.3 + - - +
79A ALA 3.9 3.8 - - - +
80A ARG 3.3 0.2 - - - -
81A ALA* 1.3 76.4 - - - +
83A ARG* 1.3 64.7 + - - +
85A LEU* 3.3 21.9 + - - +
86A LEU* 3.6 14.2 + - - +
133A LEU* 3.7 35.2 - - + +
134A VAL* 4.6 5.9 - - + +
137A ALA* 4.2 2.4 - - - +
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Residues in contact with ARG 83 (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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79A ALA 3.2 14.5 + - - +
80A ARG* 4.2 21.6 - - - +
82A ALA* 1.3 79.4 - - - +
84A CYS* 1.3 83.1 + - - +
86A LEU* 3.3 7.4 + - - +
87A GLU* 3.2 49.8 + - - +
137A ALA* 4.3 15.7 - - + +
140A GLN* 5.2 7.2 - - - +
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Residues in contact with CYS 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ARG* 3.3 19.4 + - + +
81A ALA* 4.3 4.3 - - - +
83A ARG* 1.3 92.9 - - - +
85A LEU* 1.3 55.3 + - - +
87A GLU* 3.1 13.1 + - - +
88A GLN* 2.8 57.1 + - - +
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Residues in contact with LEU 85 (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 LEU* 4.5 10.5 - - + -
17A THR* 4.4 14.4 - - + -
41A CYS* 3.6 32.1 - - + -
72A PHE* 3.6 35.0 - - + -
73A GLN 5.1 0.4 - - - +
74A ALA* 4.1 11.9 - - + -
76A VAL* 5.1 2.2 - - + -
81A ALA 3.2 15.9 + - - +
82A ALA* 3.3 13.9 - - - +
83A ARG 3.2 0.2 - - - -
84A CYS* 1.3 76.9 - - - +
86A LEU* 1.3 70.7 + - + +
88A GLN* 3.3 11.5 + - - +
89A VAL* 3.1 32.0 + - + +
134A VAL* 5.1 7.9 - - + -
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Residues in contact with LEU 86 (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 LEU* 3.9 20.4 - - + -
82A ALA 3.6 14.4 - - - +
83A ARG 3.3 9.5 + - - +
85A LEU* 1.3 85.6 - - + +
87A GLU* 1.3 59.0 + - + +
89A VAL* 3.4 4.5 + - + +
90A GLN* 2.9 44.6 + - - +
97A PRO* 3.7 35.7 - - + -
134A VAL* 4.7 7.9 - - + +
137A ALA* 3.5 34.3 - - + +
138A ALA* 3.9 15.7 - - - +
141A ALA* 4.2 5.8 - - + -
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Residues in contact with GLU 87 (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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83A ARG* 3.3 44.3 + - - +
84A CYS* 3.1 14.9 + - - +
86A LEU* 1.3 76.9 - - - +
88A GLN* 1.3 59.2 + - + +
90A GLN* 3.9 22.1 + - - +
91A ALA* 3.0 31.2 + - - +
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Residues in contact with GLN 88 (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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72A PHE* 3.3 32.6 - - + +
73A GLN 4.4 14.3 + - - +
84A CYS* 2.8 41.3 + - - +
85A LEU* 3.3 8.5 + - - +
87A GLU* 1.3 73.6 - - - +
89A VAL* 1.3 57.9 + - - +
91A ALA* 3.5 4.5 + - - +
92A CYS* 3.0 31.0 + - - +
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Residues in contact with VAL 89 (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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13A LEU* 3.7 26.2 - - + -
15A LEU* 4.2 23.3 - - + -
39A ALA* 4.2 6.5 - - + -
72A PHE* 3.8 29.2 - - + -
85A LEU* 3.1 15.5 + - + +
86A LEU* 3.7 10.3 - - - +
87A GLU 3.3 0.2 - - - -
88A GLN* 1.3 75.0 - - - +
90A GLN* 1.3 64.2 + - - +
92A CYS 3.2 0.5 + - - -
93A PHE* 3.0 32.7 + - + +
95A ARG 3.9 0.4 - - - +
97A PRO* 4.0 19.1 - - + -
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Residues in contact with GLN 90 (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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86A LEU* 2.9 31.3 + - - +
87A GLU* 3.9 25.3 + - - +
89A VAL* 1.3 76.8 - - - +
91A ALA* 1.3 58.4 + - - +
94A SER* 2.9 29.6 + - - -
95A ARG 3.5 9.1 + - - +
96A PRO* 4.1 23.8 - - + -
97A PRO* 5.0 1.6 - - + -
141A ALA* 3.4 30.8 - - + +
145A ASN* 4.4 11.3 - - - +
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Residues in contact with ALA 91 (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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87A GLU 3.0 19.3 + - - +
88A GLN* 3.9 5.2 - - - +
90A GLN* 1.3 76.8 - - - +
92A CYS* 1.3 63.8 + - - +
93A PHE 3.6 0.3 + - - -
94A SER* 4.0 7.4 + - - -
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Residues in contact with CYS 92 (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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70A ALA* 4.2 13.0 - - - -
72A PHE* 4.0 7.4 - - + -
88A GLN 3.0 19.1 + - - +
89A VAL 3.2 4.0 + - - +
91A ALA* 1.3 78.8 - - - +
93A PHE* 1.3 88.3 + - + +
94A SER* 5.3 0.4 + - - -
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Residues in contact with PHE 93 (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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13A LEU* 3.8 40.2 - - + -
37A THR* 3.8 13.7 - - + -
38A VAL 4.8 0.2 - - - -
39A ALA* 4.2 6.5 - - + -
68A ASN* 3.1 27.6 - - + -
70A ALA* 3.7 26.5 - - + -
72A PHE* 3.9 19.5 - + - -
89A VAL* 3.0 26.1 + - + +
92A CYS* 1.3 93.8 - - + +
94A SER* 1.3 73.4 + - - +
95A ARG* 3.2 16.2 + - + +
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Residues in contact with SER 94 (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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90A GLN 2.9 15.0 + - - -
91A ALA 4.0 6.3 + - - -
92A CYS 3.7 1.1 + - - -
93A PHE* 1.3 80.5 - - - +
95A ARG* 1.3 59.5 + - - +
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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