Contacts of the helix formed by residues 76 - 92 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C GLU 3.3 18.7 + - - -
53C GLN* 3.0 30.3 + - - +
54C GLN 4.6 0.4 - - - -
55C GLY* 3.7 21.4 + - - +
74C LYS 4.2 1.0 + - - +
75C MET* 1.3 77.5 - - - +
77C GLN* 1.3 66.7 + - - +
78C ALA* 3.2 7.2 - - + +
79C GLU* 3.1 13.1 + - + +
80C ALA* 3.0 18.7 + - - +
273C PHE* 4.2 0.2 - - - -
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Residues in contact with GLN 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C MET 3.8 1.4 + - - -
76C LYS* 1.3 72.4 - - - +
78C ALA* 1.3 57.2 + - - +
80C ALA* 3.2 2.4 + - - +
81C GLU* 2.8 56.5 + - + +
270C LEU* 4.4 16.8 + - + +
273C PHE* 3.4 51.5 + - + +
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Residues in contact with ALA 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C LYS* 3.2 6.1 - - + +
77C GLN* 1.3 79.4 - - - +
79C GLU* 1.3 58.2 + - - +
81C GLU* 3.7 9.6 - - - +
82C GLU* 3.0 28.2 + - - +
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Residues in contact with GLU 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C GLN 5.3 1.4 - - - +
55C GLY* 4.2 15.8 - - - +
75C MET* 3.7 24.5 - - + +
76C LYS* 3.1 16.5 + - + +
78C ALA* 1.3 75.5 - - - +
80C ALA* 1.3 68.0 + - - +
82C GLU* 3.9 6.3 - - + +
83C PHE* 2.9 27.0 + - + +
117C LYS* 2.9 37.9 + - - +
120C LYS* 4.4 5.5 + - - +
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Residues in contact with ALA 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C MET* 3.6 11.4 - - - -
76C LYS 3.0 9.3 + - - +
77C GLN* 3.2 7.6 + - + +
79C GLU* 1.3 77.2 - - - +
81C GLU* 1.3 57.3 + - - +
83C PHE* 3.7 1.4 - - - +
84C VAL* 2.9 35.2 + - - +
121C LEU* 3.8 20.6 - - + -
269C PHE* 4.1 10.1 - - + -
273C PHE* 3.7 30.1 - - + -
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Residues in contact with GLU 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C GLN* 2.8 47.5 + - - +
78C ALA* 3.7 8.2 + - - +
80C ALA* 1.3 76.6 - - - +
82C GLU* 1.3 62.3 + - - +
84C VAL* 4.1 0.9 - - - +
85C GLN* 3.0 25.3 + - - +
266C ASN* 5.4 4.2 + - - +
269C PHE* 4.1 9.8 - - + -
270C LEU* 3.7 34.1 - - + +
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Residues in contact with GLU 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C ALA 3.0 18.9 + - - +
79C GLU* 3.9 7.0 - - - +
80C ALA 3.3 0.2 - - - -
81C GLU* 1.3 76.9 - - - +
83C PHE* 1.3 63.3 + - - +
85C GLN* 3.5 12.6 + - - +
86C THR* 3.1 42.6 + - - +
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Residues in contact with PHE 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C MET* 5.4 2.7 - - - -
79C GLU* 2.9 24.2 + - + +
80C ALA* 3.8 2.5 - - - +
82C GLU* 1.3 80.5 + - - +
84C VAL* 1.3 75.1 + - + +
86C THR* 3.4 5.5 + - - +
87C LEU* 2.9 50.1 + - + +
114C VAL* 3.9 17.3 - - + -
117C LYS* 3.5 46.0 - - + -
118C VAL* 3.6 32.1 - - + -
121C LEU* 4.8 7.0 - - + -
249C LEU* 4.8 3.6 - - + -
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Residues in contact with VAL 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C ALA 2.9 20.4 + - - +
81C GLU 4.1 0.9 - - - +
83C PHE* 1.3 83.5 - - + +
85C GLN* 1.3 59.2 + - - +
87C LEU* 3.7 4.8 - - + +
88C GLY* 2.8 28.1 + - - -
121C LEU* 4.0 21.8 - - + -
249C LEU* 3.4 37.2 - - + +
250C LEU* 3.6 16.5 - - + +
266C ASN* 3.7 7.6 - - - +
269C PHE* 3.6 27.1 - - + -
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Residues in contact with GLN 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C GLU 3.0 19.4 + - - +
82C GLU* 3.7 12.3 + - - +
84C VAL* 1.3 77.6 - - - +
86C THR* 1.3 57.9 + - - +
88C GLY* 3.2 2.4 + - - -
89C GLN* 2.9 52.8 + - + +
266C ASN* 4.8 8.9 - - - +
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Residues in contact with THR 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C GLU* 3.1 30.6 + - - +
83C PHE* 3.8 7.4 - - - -
85C GLN* 1.3 75.8 + - - +
87C LEU* 1.3 64.3 + - - +
89C GLN* 3.3 20.3 + - - +
90C SER* 3.1 22.6 + - - -
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Residues in contact with LEU 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C PHE* 2.9 42.2 + - + +
84C VAL* 3.7 6.1 - - + +
86C THR* 1.3 76.1 - - - +
88C GLY* 1.3 64.2 + - - +
90C SER* 3.1 9.9 + - - +
91C LEU* 3.1 25.7 + - + +
108C ILE* 4.4 20.2 - - + -
114C VAL* 4.0 26.2 - - + -
118C VAL* 4.6 2.5 - - + -
232C LEU* 3.7 33.4 - - + -
249C LEU* 5.5 1.3 - - + -
250C LEU* 3.9 14.4 - - + -
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Residues in contact with GLY 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C VAL 2.8 17.6 + - - -
85C GLN* 3.6 2.0 - - - -
87C LEU* 1.3 76.2 - - - +
89C GLN* 1.3 61.9 + - - +
91C LEU* 3.3 4.3 + - - +
92C ALA* 3.2 21.1 + - - +
250C LEU* 3.7 23.9 - - - +
264C ILE* 4.1 15.6 - - - +
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Residues in contact with GLN 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C GLN* 2.9 37.1 + - + +
86C THR* 3.6 27.2 + - - +
87C LEU 3.2 0.2 - - - -
88C GLY* 1.3 76.1 - - - +
90C SER* 1.3 62.9 + - - +
92C ALA* 3.0 24.4 + - - +
93C ASN* 5.4 0.3 - - - +
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Residues in contact with SER 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C THR* 3.1 14.3 + - - -
87C LEU* 3.1 17.1 + - - +
89C GLN* 1.3 76.7 - - - +
91C LEU* 1.3 67.6 + - - +
92C ALA 3.6 0.3 + - - -
93C ASN* 3.8 9.9 + - - +
96C ARG* 3.1 26.8 + - - -
108C ILE* 4.6 6.9 - - - +
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Residues in contact with LEU 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C LEU* 3.1 19.9 + - + +
88C GLY 3.7 4.7 - - - +
89C GLN 3.1 0.4 - - - -
90C SER* 1.3 76.4 - - - +
92C ALA* 1.3 51.9 + - - +
93C ASN 2.8 17.4 + - - +
96C ARG* 3.5 35.4 - - - +
103C VAL* 4.1 5.1 - - + +
104C TYR 4.4 0.4 - - - +
105C LEU* 3.6 35.2 - - + -
108C ILE* 4.1 15.5 - - + -
232C LEU* 5.5 1.8 - - + -
233C VAL* 4.2 10.3 - - + -
250C LEU* 3.7 26.5 - - + -
262C ILE* 3.7 10.9 - - - +
264C ILE* 3.2 26.5 - - + +
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Residues in contact with ALA 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C GLY 3.2 11.5 + - - +
89C GLN* 3.0 19.9 + - - +
91C LEU* 1.3 73.3 - - - +
93C ASN* 1.3 56.8 + - - +
94C PRO* 3.6 9.0 - - - +
262C ILE* 3.9 25.1 - - - +
264C ILE* 4.3 13.0 - - + +
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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
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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