Contacts of the helix formed by residues 76 - 93 (chain A) in PDB entry 1P4A
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 LYS 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A GLU* 3.1 31.1 + - - +
53A GLN* 4.3 7.1 + - - +
55A GLY* 4.0 23.4 + - - +
74A LYS 4.2 0.6 - - - -
75A MET* 1.3 79.3 - - - +
77A GLN* 1.3 66.5 + - - +
78A ALA* 4.2 8.3 - - + +
79A GLU* 3.2 14.7 + - + +
80A ALA* 3.0 18.2 + - - +
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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
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75A MET 3.7 1.4 + - - -
76A LYS* 1.3 72.8 - - - +
78A ALA* 1.3 57.1 + - - +
80A ALA* 3.1 1.8 + - - +
81A GLU* 2.8 57.4 + - - +
270A LEU* 4.0 20.6 - - + +
273A PHE* 3.8 43.0 + - + +
274A LYS* 4.8 12.5 - - - +
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Residues in contact with ALA 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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76A LYS* 3.2 7.0 - - + +
77A GLN* 1.3 79.4 - - - +
79A GLU* 1.3 57.2 + - - +
81A GLU* 3.5 11.3 + - - +
82A GLU* 3.1 28.1 + - - +
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Residues in contact with GLU 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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54A GLN 5.6 0.9 - - - +
55A GLY* 4.4 14.6 - - - +
75A MET* 3.9 25.1 - - + +
76A LYS* 3.2 16.1 + - + +
78A ALA* 1.3 76.4 - - - +
80A ALA* 1.3 56.4 + - - +
82A GLU* 3.7 7.3 - - + +
83A PHE* 2.7 37.6 + - + +
117A LYS* 2.8 34.0 + - - +
120A LYS* 4.9 3.3 + - - -
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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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75A MET* 3.7 19.0 - - - -
76A LYS 3.0 10.5 + - - +
77A GLN* 3.5 7.2 - - - +
79A GLU* 1.3 77.0 - - - +
81A GLU* 1.3 58.1 + - - +
83A PHE* 3.8 1.0 - - - +
84A VAL* 2.9 36.2 + - - +
121A LEU* 3.9 10.3 - - + -
269A PHE* 4.2 6.7 - - + -
273A PHE* 3.6 34.8 - - + -
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Residues in contact with GLU 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* 2.8 44.4 + - - +
78A ALA* 3.8 10.3 - - - +
80A ALA* 1.3 76.2 - - - +
82A GLU* 1.3 61.0 + - - +
84A VAL* 4.0 1.7 - - - +
85A GLN* 3.1 24.1 + - - +
266A ASN* 5.2 3.1 - - - +
269A PHE* 4.1 11.8 - - + -
270A LEU* 3.4 35.2 - - + +
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Residues in contact with GLU 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 ALA 3.1 17.1 + - - +
79A GLU* 3.7 8.6 - - + +
81A GLU* 1.3 77.2 - - - +
83A PHE* 1.3 64.8 + - - +
85A GLN* 3.3 6.9 + - - +
86A THR* 3.1 33.1 + - - +
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Residues in contact with PHE 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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75A MET* 5.2 2.5 - - - -
79A GLU* 2.7 27.9 + - + +
80A ALA* 3.8 3.4 - - - +
82A GLU* 1.3 74.9 - - - +
84A VAL* 1.3 66.5 + - + +
86A THR* 3.5 7.7 + - + -
87A LEU* 2.9 48.1 + - + +
113A SER 5.1 0.4 - - - -
114A VAL* 4.1 18.6 - - + -
117A LYS* 3.4 44.4 - - + -
118A VAL* 3.6 32.3 - - + -
121A LEU* 4.6 10.3 - - + -
249A LEU* 4.8 4.3 - - + -
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Residues in contact with VAL 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 ALA 2.9 20.4 + - - +
81A GLU 4.0 1.1 - - - +
83A PHE* 1.3 79.2 - - + +
85A GLN* 1.3 57.1 + - - +
87A LEU* 3.8 5.3 - - + +
88A GLY* 2.8 27.9 + - - -
121A LEU* 4.2 17.3 - - + -
249A LEU* 3.5 43.3 - - + +
250A LEU* 3.7 14.2 - - + +
266A ASN* 3.8 10.1 - - - +
269A PHE* 3.6 28.0 - - + -
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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 GLU 3.1 17.4 + - - +
82A GLU* 3.7 6.7 - - - +
84A VAL* 1.3 77.8 - - - +
86A THR* 1.3 64.3 + - - +
88A GLY* 3.2 2.9 + - - -
89A GLN* 2.9 50.4 + - - +
266A ASN* 4.7 11.6 + - - +
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Residues in contact with THR 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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82A GLU* 3.1 23.0 + - - +
83A PHE* 3.6 9.1 - - + -
85A GLN* 1.3 77.9 - - - +
87A LEU* 1.3 63.3 + - - +
89A GLN* 3.2 14.9 + - - +
90A SER* 3.1 20.6 + - - -
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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
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83A PHE* 2.9 41.8 + - + +
84A VAL* 3.8 5.8 - - - +
86A THR* 1.3 76.6 - - - +
88A GLY* 1.3 63.9 + - - +
90A SER* 3.0 10.8 + - - +
91A LEU* 3.0 27.1 + - + +
108A ILE* 4.0 28.0 - - + -
114A VAL* 4.3 15.7 - - + -
118A VAL* 4.5 2.7 - - + -
232A LEU* 3.6 33.9 - - + -
249A LEU* 5.1 2.7 - - + -
250A LEU* 3.9 16.2 - - + -
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Residues in contact with GLY 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 VAL 2.8 19.2 + - - -
85A GLN* 3.5 4.7 - - - -
87A LEU* 1.3 72.4 - - - +
89A GLN* 1.3 57.4 + - - +
91A LEU* 3.4 4.0 - - - +
92A ALA* 3.1 26.7 + - - +
250A LEU* 3.7 23.9 - - - +
264A ILE* 3.8 13.2 - - - +
266A ASN* 6.0 0.2 - - - -
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Residues in contact with GLN 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 45.8 + - - +
86A THR* 3.6 15.5 + - - +
87A LEU 3.1 0.4 - - - -
88A GLY* 1.3 74.5 - - - +
90A SER* 1.3 66.7 + - - +
92A ALA* 3.4 14.4 + - - +
93A ASN* 3.7 8.0 + - - +
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Residues in contact with SER 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 THR* 3.1 11.3 + - - -
87A LEU* 3.0 14.7 + - - +
89A GLN* 1.3 77.4 - - - +
91A LEU* 1.3 60.4 + - - +
93A ASN* 3.3 16.0 + - - +
96A ARG* 3.0 35.9 + - - -
108A ILE* 3.9 14.7 - - - +
111A LYS* 5.7 0.6 + - - -
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Residues in contact with LEU 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 LEU* 3.0 27.7 + - + +
88A GLY* 3.4 12.6 - - - +
90A SER* 1.3 78.4 + - - +
92A ALA* 1.3 59.4 + - - +
93A ASN 3.5 1.9 + - - +
96A ARG* 3.6 16.1 - - - +
103A VAL* 4.2 12.3 - - + +
105A LEU* 3.0 36.8 - - + -
108A ILE* 4.8 14.6 - - + -
232A LEU* 6.1 0.9 - - + -
233A VAL* 4.6 13.5 - - + -
250A LEU* 3.9 19.7 - - + -
252A LEU* 4.8 6.3 - - + -
262A ILE* 4.0 5.9 - - - +
264A ILE* 3.3 23.1 - - + +
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Residues in contact with ALA 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 GLY 3.1 16.4 + - - +
89A GLN* 3.4 9.2 + - - +
90A SER 3.2 1.2 - - - -
91A LEU* 1.3 75.4 - - - +
93A ASN* 1.3 65.5 + - - +
94A PRO* 3.1 5.9 - - - +
262A ILE* 3.0 29.1 + - - +
264A ILE* 3.4 17.0 - - + +
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Residues in contact with ASN 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 GLN 3.7 6.2 + - - +
90A SER* 3.3 17.7 + - - +
91A LEU 3.3 0.2 - - - -
92A ALA* 1.3 76.0 - - - +
94A PRO* 1.3 76.3 - - - +
95A GLU* 2.9 42.3 + - - +
96A ARG* 3.0 29.0 + - - +
262A ILE* 4.1 3.3 - - - +
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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