Contacts of the helix formed by residues 75 - 88 (chain A) in PDB entry 1P7D
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
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Residue Dist Surf HB Arom Phob DC
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74A MET* 1.3 79.0 - - - +
76A LEU* 1.3 65.8 + - - +
78A SER* 3.0 25.1 + - - -
79A TRP* 3.0 12.9 + - - +
113A ASP* 2.7 35.7 - - - -
114A ALA 3.5 2.5 - - - -
115A PRO* 4.2 0.9 - - - -
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Residues in contact with LEU 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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75A THR* 1.3 70.4 - - - +
77A HIS* 1.3 55.6 + - + +
79A TRP* 3.0 13.4 + - + +
80A LEU* 2.8 59.3 + - + +
107A ILE* 4.5 11.2 - - + +
111A LEU* 3.5 42.4 - - + +
112A PRO 3.6 15.3 - - - +
113A ASP 3.3 0.8 + - - -
114A ALA 2.9 18.9 + - - +
115A PRO* 4.7 3.9 + - - +
147A LEU* 5.2 1.3 - - + -
151A PHE* 4.6 22.0 - - + -
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Residues in contact with HIS 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A THR 3.3 0.4 - - - -
76A LEU* 1.3 84.2 - - + +
78A SER* 1.3 65.5 + - - +
80A LEU* 2.9 16.7 + - + +
81A ASP* 3.1 17.5 + - - +
108A ARG* 3.8 45.1 + - + +
111A LEU 3.2 12.6 + - - -
112A PRO 3.1 29.7 + - - -
113A ASP* 3.5 27.1 + - + +
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Residues in contact with SER 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A MET* 3.7 12.1 - - - +
75A THR* 3.0 32.0 + - - -
77A HIS* 1.3 77.7 - - - +
79A TRP* 1.3 59.6 + - - +
81A ASP* 3.3 14.6 + - - +
82A ARG* 3.3 17.0 + - - +
113A ASP* 4.2 1.6 + - - -
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Residues in contact with TRP 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A MET* 3.2 37.2 - - + -
75A THR 3.0 12.5 + - - +
76A LEU* 3.0 18.4 + - + +
78A SER* 1.3 75.5 + - - +
80A LEU* 1.3 71.8 + - + +
81A ASP 3.0 2.0 - - - -
82A ARG* 3.0 34.5 + - + -
83A TYR* 2.8 38.2 + + + +
86A ILE* 4.3 4.7 - - + -
150A ALA* 3.3 23.7 + - + +
151A PHE* 6.1 2.2 - + - -
153A GLU* 3.6 18.2 - - + -
154A ALA* 3.2 42.0 - - + +
157A GLU* 3.4 24.0 - - - -
159A HIS* 3.8 9.2 - + - -
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Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LEU* 2.8 38.9 + - + +
77A HIS* 2.9 9.2 + - + +
79A TRP* 1.3 84.7 - - + +
81A ASP* 1.3 57.5 + - - +
83A TYR* 3.2 9.3 + - + +
84A GLU* 2.9 32.0 + - - +
104A ILE* 4.0 22.7 - - + +
107A ILE* 4.0 25.4 - - + -
108A ARG* 3.7 41.7 - - + +
147A LEU* 5.7 1.3 - - + -
150A ALA* 4.7 15.5 - - + -
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Residues in contact with ASP 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 HIS* 3.1 17.7 + - - +
78A SER* 3.4 14.8 - - - +
79A TRP 3.0 0.2 - - - -
80A LEU* 1.3 74.9 - - - +
82A ARG* 1.3 63.8 + - - +
84A GLU* 3.2 27.8 - - - +
85A LYS* 3.4 28.7 + - - +
108A ARG* 3.0 20.7 + - - -
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Residues in contact with ARG 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 MET* 5.5 4.3 - - - -
78A SER 3.3 7.5 + - - +
79A TRP* 3.0 38.5 + - + +
81A ASP* 1.3 78.6 - - - +
83A TYR* 1.3 62.3 + - - +
85A LYS* 3.3 31.8 + - - +
86A ILE* 3.1 46.4 + - - +
157A GLU* 2.8 30.5 + - - +
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Residues in contact with TYR 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 TRP* 2.8 26.5 + + - +
80A LEU* 3.4 9.4 - - + +
82A ARG* 1.3 79.2 - - - +
84A GLU* 1.3 55.8 + - - +
86A ILE* 3.0 15.0 - - + +
87A LEU* 2.9 56.7 + - + +
90A ARG* 4.5 1.1 - - - -
104A ILE* 3.5 26.5 - - + -
146A THR* 3.9 14.3 + - + +
149A ASP* 2.5 32.3 + - - +
150A ALA* 3.4 39.2 + - + -
153A GLU* 3.7 28.9 - - + -
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Residues in contact with GLU 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 LEU 2.9 14.1 + - - +
81A ASP* 3.2 36.3 - - - +
83A TYR* 1.3 74.6 - - - +
85A LYS* 1.3 61.8 + - + +
87A LEU* 3.2 11.6 + - - +
88A ALA* 2.8 29.3 + - - +
97A LEU* 5.2 1.9 - - - +
101A MET* 3.2 42.5 - - - +
104A ILE* 3.8 15.4 - - + +
108A ARG* 3.6 16.0 + - - -
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Residues in contact with LYS 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 ASP* 3.4 27.1 + - - +
82A ARG* 3.3 30.5 + - - +
84A GLU* 1.3 77.8 - - + +
86A ILE* 1.3 64.1 + - - +
88A ALA* 3.1 21.5 - - - +
89A SER* 3.8 5.5 + - - -
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Residues in contact with ILE 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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79A TRP* 4.3 13.5 - - + -
82A ARG* 3.1 46.6 + - - +
83A TYR* 3.0 17.2 + - + +
85A LYS* 1.3 77.0 - - - +
87A LEU* 1.3 66.8 + - - +
89A SER* 2.8 28.5 + - - -
90A ARG* 4.2 14.7 - - + +
153A GLU* 3.7 35.2 - - + +
157A GLU* 4.2 7.0 - - + +
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Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A TYR* 2.9 53.3 + - + +
84A GLU* 3.5 8.5 - - + +
86A ILE* 1.3 80.3 - - - +
88A ALA* 1.3 56.1 + - - +
89A SER 2.7 23.9 + - - +
90A ARG* 3.7 38.2 - - - +
92A ILE* 4.0 9.1 - - - +
97A LEU* 4.8 12.1 - - + +
100A TYR* 4.0 34.8 - - + -
101A MET* 5.6 0.4 - - - -
104A ILE* 3.5 20.4 - - + -
146A THR* 5.4 1.3 - - + -
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Residues in contact with ALA 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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84A GLU 2.8 16.9 + - - +
85A LYS* 3.1 19.7 - - - +
86A ILE 3.1 0.2 + - - -
87A LEU* 1.3 71.2 - - - +
89A SER* 1.3 59.5 + - - +
92A ILE* 5.7 0.9 - - - +
97A LEU* 4.5 24.4 - - + +
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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