Contacts of the helix formed by residues 76 - 92 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52B GLU 2.9 29.0 + - - -
53B GLN* 3.3 19.2 + - - +
54B GLN 4.7 0.4 - - - -
55B GLY* 3.8 20.5 + - - +
74B LYS 4.2 0.8 + - - -
75B MET* 1.3 77.7 - - - +
77B GLN* 1.3 67.2 + - - +
78B ALA* 4.3 7.6 - - + +
79B GLU* 3.1 15.4 + - + +
80B ALA* 2.9 19.4 + - - +
273B PHE* 4.0 0.4 - - - -
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Residues in contact with GLN 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B LYS* 1.3 71.5 - - - +
78B ALA* 1.3 57.5 + - - +
80B ALA* 3.2 3.3 + - - +
81B GLU* 2.9 53.3 + - - +
270B LEU* 4.1 22.6 + - + +
273B PHE* 3.6 45.2 + - + +
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Residues in contact with ALA 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B LYS* 3.2 5.9 - - + +
77B GLN* 1.3 76.6 - - - +
79B GLU* 1.3 65.7 + - - +
81B GLU* 4.1 7.8 - - - +
82B GLU* 3.1 24.8 + - - +
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Residues in contact with GLU 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B GLN 5.5 0.3 - - - +
55B GLY* 3.9 19.2 - - - +
75B MET* 3.6 26.2 - - + +
76B LYS* 3.1 17.0 + - + +
78B ALA* 1.3 76.7 - - - +
80B ALA* 1.3 67.5 + - - +
82B GLU* 3.4 8.2 + - - +
83B PHE* 2.9 26.4 + - + +
117B LYS* 2.9 35.6 + - + +
120B LYS* 4.4 4.0 + - - -
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Residues in contact with ALA 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B MET* 3.6 19.2 - - - -
76B LYS 2.9 12.6 + - - +
77B GLN 3.5 7.6 - - - +
79B GLU* 1.3 76.9 - - - +
81B GLU* 1.3 57.3 + - - +
83B PHE* 3.3 1.5 + - - +
84B VAL* 2.9 34.1 + - - +
121B LEU* 4.1 9.6 - - + -
269B PHE* 4.1 13.9 - - + -
273B PHE* 3.7 25.4 - - + -
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Residues in contact with GLU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B GLN* 2.9 49.5 + - - +
78B ALA* 4.1 7.3 + - - +
80B ALA* 1.3 72.0 - - - +
82B GLU* 1.3 57.9 + - - +
84B VAL* 4.0 0.7 - - - +
85B GLN* 2.9 32.5 + - - +
266B ASN* 5.3 5.5 + - - +
269B PHE* 4.0 12.1 - - + -
270B LEU* 3.7 34.6 - - + +
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Residues in contact with GLU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B ALA 3.1 16.9 + - - +
79B GLU* 3.8 6.3 - - - +
81B GLU* 1.3 78.5 - - - +
83B PHE* 1.3 58.4 + - - +
85B GLN* 3.6 14.3 + - - +
86B THR* 3.0 39.0 + - - +
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Residues in contact with PHE 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B MET* 5.2 4.0 - - - -
79B GLU* 2.9 23.9 + - + +
80B ALA* 3.7 3.4 - - - +
82B GLU* 1.3 76.7 - - - +
84B VAL* 1.3 70.1 + - + +
86B THR* 3.3 7.0 + - - -
87B LEU* 2.9 46.5 + - + +
114B VAL* 3.8 26.5 - - + -
117B LYS* 3.5 44.9 - - + -
118B VAL* 3.7 26.2 - - + -
121B LEU* 4.7 7.6 - - + -
249B LEU* 4.8 5.4 - - + -
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Residues in contact with VAL 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B ALA 2.9 20.8 + - - +
81B GLU 4.0 1.1 - - - +
83B PHE* 1.3 79.0 - - + +
85B GLN* 1.3 56.3 + - - +
87B LEU* 3.2 6.7 + - - +
88B GLY* 2.7 33.3 + - - -
121B LEU* 3.8 23.8 - - + -
249B LEU* 3.3 34.1 - - + +
250B LEU* 3.5 16.6 - - + +
266B ASN* 3.7 16.4 - - - +
269B PHE* 3.7 19.7 - - + -
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Residues in contact with GLN 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B GLU 2.9 19.3 + - - +
82B GLU* 3.6 15.0 + - - +
84B VAL* 1.3 79.6 - - - +
86B THR* 1.3 66.4 + - - +
88B GLY* 3.2 0.9 + - - -
89B GLN* 2.9 50.6 + - + +
250B LEU* 5.7 0.4 - - - -
266B ASN* 4.8 7.6 - - - +
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Residues in contact with THR 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B GLU* 3.0 23.6 + - - +
83B PHE* 3.7 8.9 - - - -
84B VAL 3.3 0.2 - - - -
85B GLN* 1.3 80.3 + - - +
87B LEU* 1.3 63.1 + - - +
89B GLN* 3.4 17.5 + - - +
90B SER* 3.2 22.3 + - - -
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Residues in contact with LEU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B PHE* 2.9 41.3 + - + +
84B VAL* 3.6 7.2 - - - +
86B THR* 1.3 78.3 - - - +
88B GLY* 1.3 62.5 + - - +
90B SER* 3.2 10.3 + - - +
91B LEU* 3.0 23.5 + - + +
108B ILE* 3.9 35.4 - - + -
114B VAL* 4.5 12.8 - - + -
118B VAL* 4.5 3.4 - - + -
232B LEU* 3.8 32.8 - - + -
249B LEU* 5.3 2.7 - - + -
250B LEU* 4.0 13.9 - - + -
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Residues in contact with GLY 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B VAL 2.7 20.0 + - - -
85B GLN* 3.7 1.6 - - - -
87B LEU* 1.3 73.3 - - - +
89B GLN* 1.3 56.3 + - - +
91B LEU* 3.0 5.3 + - - +
92B ALA* 2.8 29.3 + - - +
250B LEU* 3.6 22.4 - - - +
264B ILE* 3.8 14.5 - - - +
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Residues in contact with GLN 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B GLN* 2.9 41.1 + - + +
86B THR* 3.6 23.5 + - - +
88B GLY* 1.3 76.1 - - - +
90B SER* 1.3 60.0 + - - +
92B ALA* 3.2 21.7 + - - +
93B ASN* 4.5 0.9 + - - +
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Residues in contact with SER 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B THR* 3.2 12.7 + - - -
87B LEU* 3.2 13.2 + - - +
89B GLN* 1.3 77.4 - - - +
91B LEU* 1.3 62.5 + - - +
93B ASN* 3.8 9.1 + - - +
96B ARG* 2.8 28.1 + - - -
108B ILE* 3.9 17.7 - - - +
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Residues in contact with LEU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B LEU* 3.0 18.3 + - + +
88B GLY* 3.0 9.8 + - - +
90B SER* 1.3 73.5 + - - +
92B ALA* 1.3 51.5 - - - +
93B ASN 2.7 22.6 + - - +
96B ARG* 3.7 19.6 - - - +
103B VAL* 4.6 8.9 - - + +
104B TYR 4.5 0.7 - - - +
105B LEU* 3.7 19.3 - - + -
108B ILE* 3.2 33.7 - - + -
232B LEU* 6.0 0.9 - - + -
233B VAL* 3.8 22.0 - - + -
250B LEU* 3.7 25.1 - - + -
262B ILE* 4.0 6.2 - - - +
264B ILE* 3.5 25.2 - - + +
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Residues in contact with ALA 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B GLY 2.8 14.3 + - - +
89B GLN* 3.2 17.4 + - - +
91B LEU* 1.3 72.2 - - - +
93B ASN* 1.3 58.2 + - - +
94B PRO* 3.8 7.1 - - - +
262B ILE* 3.9 19.3 - - - +
263B GLU* 5.7 0.2 - - - -
264B ILE* 3.7 21.5 - - + +
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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