Contacts of the helix formed by residues 76 - 92 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52D GLU 3.4 19.3 - - - -
53D GLN* 2.8 29.7 + - - +
54D GLN 4.2 1.2 - - - -
55D GLY* 3.7 20.9 + - - +
74D LYS 4.1 1.0 + - - -
75D MET* 1.3 77.3 - - - +
77D GLN* 1.3 66.0 + - - +
78D ALA* 4.3 8.5 - - + +
79D GLU* 3.1 15.0 + - + +
80D ALA* 3.0 17.5 + - - +
273D PHE* 4.2 0.2 - - - -
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Residues in contact with GLN 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D MET 3.6 1.6 + - - -
76D LYS* 1.3 71.9 - - - +
78D ALA* 1.3 57.3 + - - +
80D ALA* 3.1 2.8 + - + +
81D GLU* 3.0 54.0 + - + +
270D LEU* 4.4 11.7 - - + +
273D PHE* 3.7 47.7 - - + +
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Residues in contact with ALA 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D LYS* 3.2 6.5 - - + +
77D GLN* 1.3 79.3 - - - +
79D GLU* 1.3 61.7 + - - +
81D GLU* 3.8 7.9 + - - +
82D GLU* 3.2 22.7 + - - +
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Residues in contact with GLU 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D GLN 5.7 0.2 - - - +
55D GLY* 4.2 15.2 - - - +
75D MET* 3.6 27.2 - - + +
76D LYS* 3.1 17.2 + - + +
78D ALA* 1.3 76.6 - - - +
80D ALA* 1.3 62.1 + - - +
82D GLU* 3.4 8.5 + - + +
83D PHE* 2.9 30.3 + - + +
117D LYS* 3.3 33.8 + - + +
120D LYS* 4.7 4.0 + - - +
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Residues in contact with ALA 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D MET* 3.6 21.5 - - - -
76D LYS 3.0 7.9 + - - +
77D GLN 3.5 7.4 - - - +
79D GLU* 1.3 76.1 - - - +
81D GLU* 1.3 54.5 + - - +
83D PHE* 3.2 2.8 + - - +
84D VAL* 2.8 40.8 + - - +
121D LEU* 4.0 12.8 - - + -
269D PHE* 4.3 5.4 - - + -
273D PHE* 3.7 31.4 - - + -
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Residues in contact with GLU 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D GLN* 3.0 46.1 + - - +
78D ALA* 3.9 8.0 - - - +
80D ALA* 1.3 76.7 - - - +
82D GLU* 1.3 57.9 + - - +
84D VAL* 3.9 1.0 - - - +
85D GLN* 2.9 41.6 + - - +
266D ASN* 5.4 4.6 + - - +
269D PHE* 4.2 11.9 - - + -
270D LEU* 3.8 33.1 - - + +
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Residues in contact with GLU 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D ALA 3.2 17.0 + - - +
79D GLU* 3.9 7.1 - - - +
80D ALA 3.3 0.2 - - - -
81D GLU* 1.3 78.6 - - - +
83D PHE* 1.3 65.4 + - - +
85D GLN* 3.5 12.0 + - - +
86D THR* 3.1 30.8 + - - +
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Residues in contact with PHE 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D MET* 5.2 2.5 - - - -
79D GLU* 2.9 22.0 + - + +
80D ALA* 3.6 4.0 - - - +
82D GLU* 1.3 81.6 - - - +
84D VAL* 1.3 68.3 + - + +
86D THR* 3.4 5.8 + - + -
87D LEU* 2.9 50.9 + - + +
113D SER 5.1 0.4 - - - -
114D VAL* 3.9 17.7 - - + -
117D LYS* 3.6 42.8 - - + -
118D VAL* 3.6 39.5 - - + -
121D LEU* 4.6 8.1 - - + -
249D LEU* 4.8 4.7 - - + -
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Residues in contact with VAL 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D ALA 2.8 22.2 + - - +
81D GLU 4.0 1.1 - - - +
83D PHE* 1.3 72.9 - - + +
85D GLN* 1.3 55.9 + - - +
87D LEU* 3.2 7.1 + - + +
88D GLY* 2.7 34.0 + - - -
121D LEU* 3.9 22.2 - - + -
249D LEU* 3.4 37.9 - - + +
250D LEU* 3.8 12.6 - - + +
266D ASN* 3.6 19.7 - - - +
269D PHE* 3.6 20.6 - - + -
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Residues in contact with GLN 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D GLU* 2.9 27.0 + - - +
82D GLU* 3.6 11.6 - - - +
84D VAL* 1.3 76.0 - - - +
86D THR* 1.3 58.0 + - - +
88D GLY* 3.1 3.3 + - - -
89D GLN* 2.9 45.4 + - + +
266D ASN* 4.8 17.8 + - - +
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Residues in contact with THR 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D GLU* 3.1 22.8 + - - +
83D PHE* 3.8 7.0 - - + -
85D GLN* 1.3 74.3 - - - +
87D LEU* 1.3 67.2 + - - +
89D GLN* 3.2 20.0 + - - +
90D SER* 3.1 21.7 + - - -
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Residues in contact with LEU 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D PHE* 2.9 48.5 + - + +
84D VAL* 3.5 7.0 - - - +
86D THR* 1.3 77.7 - - - +
88D GLY* 1.3 62.7 + - - +
90D SER* 3.1 25.3 + - - +
91D LEU* 3.2 20.7 + - + +
108D ILE* 4.5 15.5 - - + -
114D VAL* 4.3 22.2 - - + -
118D VAL* 4.1 3.4 - - + -
232D LEU* 3.8 28.5 - - + -
249D LEU* 5.0 4.3 - - + -
250D LEU* 3.9 15.0 - - + -
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Residues in contact with GLY 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D VAL 2.7 14.3 + - - -
85D GLN* 3.1 4.7 + - - -
87D LEU* 1.3 73.2 - - - +
89D GLN* 1.3 56.3 + - - +
91D LEU* 3.3 2.9 + - - -
92D ALA* 3.0 31.3 + - - +
250D LEU* 3.5 26.8 - - - +
264D ILE* 3.9 13.2 - - - +
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Residues in contact with GLN 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D GLN* 2.9 29.7 + - + +
86D THR* 3.6 22.5 + - - +
88D GLY* 1.3 75.9 - - - +
90D SER* 1.3 60.6 + - - +
91D LEU 3.6 0.2 + - - -
92D ALA* 3.7 17.8 + - - +
93D ASN* 4.7 2.4 + - - +
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Residues in contact with SER 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D THR* 3.1 11.9 + - - -
87D LEU* 3.1 16.0 + - - +
89D GLN* 1.3 79.9 - - - +
91D LEU* 1.3 69.7 + - - +
92D ALA 3.4 0.2 - - - -
93D ASN* 4.1 9.8 - - - +
96D ARG* 3.0 27.1 + - - -
108D ILE* 4.1 8.3 - - - +
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Residues in contact with LEU 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D LEU* 3.2 17.5 + - + +
88D GLY 3.3 1.7 + - - +
90D SER* 1.3 77.5 + - - +
92D ALA* 1.3 56.9 + - - +
93D ASN 3.1 10.9 + - - -
96D ARG* 3.5 22.5 - - - +
103D VAL* 3.8 4.7 - - + +
105D LEU* 3.7 30.7 - - + -
108D ILE* 3.5 39.3 - - + -
232D LEU* 5.6 2.5 - - + -
233D VAL* 4.1 10.5 - - + -
250D LEU* 3.6 29.4 - - + -
262D ILE* 3.7 9.9 - - - +
264D ILE* 3.3 22.1 - - + +
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Residues in contact with ALA 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D GLY 3.0 17.1 + - - +
89D GLN* 3.7 10.5 + - - +
90D SER 3.4 1.2 - - - -
91D LEU* 1.3 74.6 - - - +
93D ASN* 1.3 57.7 + - - +
94D PRO* 4.3 2.6 - - - +
262D ILE* 3.8 26.7 - - - +
264D ILE* 3.6 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