Contacts of the helix formed by residues 75 - 96 (chain A) in PDB entry 4U7C
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 THR 75 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A GLN 4.5 5.4 - - - +
74A ILE* 1.3 75.7 - - - +
76A SER* 1.3 63.2 + - - +
77A GLN* 3.0 18.3 + - - +
78A GLN* 2.8 32.3 + - - +
79A LEU* 3.1 23.2 + - - +
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Residues in contact with SER 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ILE 4.2 0.6 + - - -
75A THR* 1.3 72.5 - - - +
77A GLN* 1.3 56.6 + - - +
79A LEU* 3.6 15.2 - - - +
80A ARG* 2.9 48.6 + - - +
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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
----------------------------------------------------------
75A THR* 3.0 12.2 + - - +
76A SER* 1.3 74.3 - - - +
78A GLN* 1.3 62.8 + - - +
79A LEU 3.0 1.3 - - - -
80A ARG* 2.5 61.8 + - - +
81A LYS* 2.9 16.5 + - + +
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Residues in contact with GLN 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLN 3.3 15.8 - - - +
74A ILE* 3.3 16.0 - - + +
75A THR* 2.8 42.9 + - - +
77A GLN* 1.3 79.8 - - + +
79A LEU* 1.3 59.1 + - - +
81A LYS* 3.5 20.0 + - - +
82A ALA* 2.9 28.8 + - - +
385A LEU* 4.1 14.2 - - + +
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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
----------------------------------------------------------
74A ILE* 4.5 16.4 - - + -
75A THR 3.1 17.9 + - - +
76A SER* 3.6 13.9 - - - +
78A GLN* 1.3 77.5 - - - +
80A ARG* 1.3 59.1 + - - +
82A ALA* 3.3 2.1 - - - +
83A GLN* 2.9 29.4 + - + +
381A ALA* 4.2 5.6 - - + -
382A LEU* 4.0 34.5 - - + +
385A LEU* 4.0 13.2 - - + -
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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
----------------------------------------------------------
76A SER* 2.9 38.5 + - - +
77A GLN* 2.5 44.0 + - - +
79A LEU* 1.3 73.6 - - - +
81A LYS* 1.3 66.5 + - - +
83A GLN* 3.2 9.3 + - + +
84A LEU* 2.9 28.7 + - + +
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Residues in contact with LYS 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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77A GLN* 2.9 15.0 + - + +
78A GLN* 3.7 20.2 - - - +
80A ARG* 1.3 74.9 - - - +
82A ALA* 1.3 62.4 + - - +
84A LEU* 3.1 13.8 + - + +
85A GLN* 3.0 45.8 + - + +
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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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78A GLN 2.9 18.8 + - - +
79A LEU* 3.3 9.4 - - - +
81A LYS* 1.3 76.4 - - - +
83A GLN* 1.3 62.9 + - - +
85A GLN* 3.1 12.0 + - - +
86A VAL* 2.9 27.5 + - - +
381A ALA* 3.9 17.9 - - + +
384A SER* 4.5 7.6 - - - +
385A LEU* 4.1 22.7 - - + -
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Residues in contact with GLN 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 LEU* 2.9 16.8 + - + +
80A ARG* 3.2 11.6 + - + +
82A ALA* 1.3 72.0 - - - +
84A LEU* 1.3 59.8 + - + +
86A VAL* 4.0 2.6 - - - +
87A ASP* 2.9 52.2 + - - +
378A GLN 4.6 5.5 + - - +
380A ARG* 3.9 32.2 + - - +
381A ALA* 3.5 21.0 + - + +
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Residues in contact with LEU 84 (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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80A ARG* 2.9 19.0 + - + +
81A LYS* 3.4 14.6 - - + +
83A GLN* 1.3 81.9 - - + +
85A GLN* 1.3 65.1 + - + +
87A ASP* 3.7 4.9 - - + +
88A ARG* 3.0 22.1 + - - +
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Residues in contact with GLN 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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81A LYS* 3.0 41.3 + - + +
82A ALA* 3.7 11.1 - - - +
84A LEU* 1.3 75.6 - - + +
86A VAL* 1.3 65.5 + - + +
88A ARG* 2.9 18.8 + - - +
89A PHE* 2.9 14.3 + - - +
392A TRP* 5.9 0.9 - - - -
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Residues in contact with VAL 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ALA 2.9 22.7 + - - +
83A GLN* 4.0 4.9 - - - +
85A GLN* 1.3 73.1 - - + +
87A ASP* 1.3 58.1 + - - +
89A PHE* 3.3 8.0 + - - +
90A ALA* 2.9 26.2 + - - +
380A ARG* 3.6 47.3 - - + +
381A ALA* 4.1 3.6 - - - -
384A SER* 3.4 34.1 - - - +
392A TRP* 4.1 21.5 - - + -
396A LEU* 4.4 6.3 - - + +
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Residues in contact with ASP 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLN* 2.9 43.7 + - - +
84A LEU* 3.7 6.0 - - + +
85A GLN 3.2 0.2 - - - -
86A VAL* 1.3 73.6 - - - +
88A ARG* 1.3 66.9 + - - +
90A ALA* 3.7 5.1 - - - +
91A MET* 2.9 24.3 + - - +
377A TYR* 4.3 5.0 + - - -
380A ARG* 2.8 36.6 + - - -
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Residues in contact with ARG 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU 3.0 12.7 + - - +
85A GLN* 2.9 12.8 + - - +
87A ASP* 1.3 76.4 - - - +
89A PHE* 1.3 62.4 + - - +
91A MET* 3.2 9.4 + - - +
92A GLU* 3.0 19.9 + - - +
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Residues in contact with PHE 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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85A GLN 2.9 10.8 + - - +
86A VAL* 3.6 9.4 - - - +
88A ARG* 1.3 77.5 - - - +
90A ALA* 1.3 55.1 + - - +
92A GLU* 2.9 16.6 + - + +
93A LEU* 2.9 58.2 + - + +
392A TRP* 4.2 12.8 - + + -
393A HIS* 3.7 44.0 - + + -
396A LEU* 3.8 17.7 - - + -
397A HIS* 4.7 7.0 - + - -
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Residues in contact with ALA 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 VAL* 2.9 21.5 + - + +
87A ASP* 3.7 13.5 - - - +
89A PHE* 1.3 69.8 - - - +
91A MET* 1.3 65.5 + - - +
93A LEU* 3.0 6.7 + - - +
94A GLU* 2.9 25.7 + - - +
377A TYR* 5.0 10.3 - - + +
380A ARG* 5.3 0.2 - - - -
396A LEU* 3.7 28.3 - - + -
400A LEU* 4.0 9.1 - - + +
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Residues in contact with MET 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 ASP 2.9 14.3 + - - +
88A ARG* 3.2 12.1 - - - +
90A ALA* 1.3 76.9 - - - +
92A GLU* 1.3 64.4 + - - +
94A GLU* 3.4 9.3 + - - -
95A GLN* 2.9 30.6 + - + +
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Residues in contact with GLU 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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88A ARG 3.0 11.4 + - - +
89A PHE* 2.9 24.7 + - + +
91A MET* 1.3 77.5 - - - +
93A LEU* 1.3 62.4 + - + +
95A GLN* 3.5 7.5 + - - +
96A SER* 3.3 18.9 + - - -
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Residues in contact with LEU 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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89A PHE* 2.9 46.1 + - + +
90A ALA 3.0 6.9 + - - +
92A GLU* 1.3 72.2 - - + +
94A GLU* 1.3 55.7 + - - +
95A GLN 3.0 4.0 - - - -
96A SER* 2.7 31.0 + - - -
97A ARG 3.2 8.1 + - - -
396A LEU* 3.7 26.5 - - + -
397A HIS* 3.6 42.6 - - + +
400A LEU* 3.9 13.2 - - + -
402A LEU* 3.9 16.2 - - + +
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Residues in contact with GLU 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 ALA 2.9 17.8 + - - +
91A MET* 4.0 10.5 - - - +
93A LEU* 1.3 72.5 - - - +
95A GLN* 1.3 61.0 + - - +
97A ARG* 3.3 49.9 + - - +
339A ARG* 2.6 38.4 + - - +
343A MET* 4.3 0.9 - - - +
400A LEU* 4.3 15.7 - - + +
402A LEU* 5.3 0.4 - - - -
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Residues in contact with GLN 95 (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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91A MET* 2.9 26.3 + - + +
92A GLU* 3.5 9.4 - - - +
93A LEU 3.0 0.2 + - - -
94A GLU* 1.3 78.7 - - - +
96A SER* 1.3 57.3 + - - +
97A ARG 3.2 6.7 + - - +
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Residues in contact with SER 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A GLU 3.3 8.9 + - - -
93A LEU* 2.7 20.7 + - - -
95A GLN* 1.3 72.2 - - - +
97A ARG* 1.3 64.7 + - - -
98A ASN* 3.4 5.5 + - - +
402A LEU* 5.4 3.0 - - - +
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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
------------------------------------------------------------
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