Contacts of the helix formed by residues 87 - 99 (chain D) in PDB entry 1PY1
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 87 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83D ASP* 3.3 22.0 - - - +
84D GLU* 3.2 38.6 + - - +
85D VAL 3.0 3.1 - - - +
86D GLY* 1.3 83.2 - - - +
88D PHE* 1.3 62.1 + - - +
89D ARG* 3.9 11.9 - - + +
90D PHE* 3.0 4.7 + - - -
91D LEU* 2.7 27.5 + - - +
131D LYS* 4.4 4.0 - - + +
2H ASP* 2.9 33.1 + - - +
3H ASP* 3.7 24.5 - - + +
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Residues in contact with PHE 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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86D GLY 4.3 0.2 + - - -
87D LYS* 1.3 70.5 - - - +
89D ARG* 1.3 62.3 + - - +
91D LEU* 3.5 18.4 - - + -
92D ASN* 2.8 49.6 + - - +
131D LYS* 3.4 46.9 - - + -
134D GLU* 3.4 27.6 - - - -
135D ALA* 4.4 5.6 - - + -
3H ASP* 3.0 15.8 + - - -
4H ILE* 3.4 26.9 - - - +
5H SEP 4.0 1.6 - - - +
6H LEU* 3.5 41.1 - - + -
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Residues in contact with ARG 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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106C ARG* 4.0 30.2 - - - +
45D PRO* 6.5 0.7 - - - -
48D THR* 6.1 0.9 - - - +
49D ARG* 6.2 5.8 - - + +
84D GLU* 5.2 9.4 - - - +
87D LYS* 3.0 11.2 - - + +
88D PHE* 1.3 78.7 - - - +
90D PHE* 1.3 56.9 + - + +
92D ASN* 4.9 0.7 - - - +
93D GLU* 3.7 20.6 + - - +
2H ASP* 2.8 31.1 + - - -
3H ASP* 2.8 16.5 + - - +
4H ILE* 3.6 40.4 - - + +
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Residues in contact with PHE 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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48D THR* 3.3 46.9 - - - +
51D LEU* 4.5 3.8 - - + -
52D ALA* 4.0 23.3 - - + -
55D ILE* 4.3 7.0 - - + -
70D LEU* 3.9 28.3 - - + -
84D GLU 3.7 17.7 - - - +
85D VAL* 3.6 42.0 - - + -
87D LYS* 3.0 2.2 + - - +
88D PHE 3.0 0.2 - - - -
89D ARG* 1.3 80.0 - - + +
91D LEU* 1.3 67.4 + - + +
92D ASN 3.3 1.8 - - - -
93D GLU* 3.2 18.0 + - + +
94D LEU* 3.5 25.2 + - + +
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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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85D VAL* 3.2 24.0 - - + +
86D GLY 4.1 1.8 - - - -
87D LYS 2.7 24.9 + - - +
88D PHE* 3.8 21.1 - - + -
90D PHE* 1.3 75.7 - - + +
92D ASN* 1.3 63.5 + - - +
94D LEU* 2.9 23.4 + - + +
95D ILE* 2.9 17.7 + - + +
119D LEU* 4.3 23.3 - - + -
122D TRP* 4.9 0.4 - - + -
131D LYS* 3.6 39.3 - - + +
132D ILE* 3.7 14.6 - - + +
135D ALA* 4.3 10.8 - - + -
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Residues in contact with ASN 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 PHE* 2.8 36.2 + - - +
89D ARG 4.9 0.4 - - - +
91D LEU* 1.3 72.6 - - - +
93D GLU* 1.3 62.3 + - - +
95D ILE* 3.3 14.1 + - - +
96D LYS* 2.8 40.4 + - - +
4H ILE* 3.3 19.6 - - + +
5H SEP 3.0 23.8 + - - -
6H LEU* 3.7 2.3 - - - +
7H LEU* 2.8 41.9 + - + +
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Residues in contact with GLU 93 (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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103C LEU* 5.9 2.5 - - - +
52D ALA* 3.6 27.5 - - + +
56D GLN* 2.7 39.5 + - - +
89D ARG 3.7 20.4 - - - +
90D PHE* 3.4 10.1 - - + +
91D LEU 3.1 0.8 - - - -
92D ASN* 1.3 79.3 - - - +
94D LEU* 1.3 60.0 + - + +
96D LYS* 3.3 30.5 + - - +
97D VAL* 3.2 27.0 + - - +
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Residues in contact with LEU 94 (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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52D ALA* 6.4 0.4 - - - -
55D ILE* 4.3 25.8 - - + -
70D LEU* 4.7 3.8 - - + -
90D PHE* 3.5 27.3 + - + +
91D LEU* 2.9 13.2 + - + +
93D GLU* 1.3 76.9 - - + +
95D ILE* 1.3 66.9 + - + +
97D VAL* 3.1 13.1 + - - +
98D VAL* 3.3 19.7 + - - +
115D ILE* 4.0 37.8 - - + +
118D LEU* 6.3 0.9 - - + -
119D LEU* 4.0 18.6 - - + -
122D TRP* 3.9 32.1 - - + -
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Residues in contact with ILE 95 (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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91D LEU* 2.9 18.1 + - + +
92D ASN* 3.6 17.7 - - - +
94D LEU* 1.3 78.3 - - + +
96D LYS* 1.3 62.8 + - - +
97D VAL 3.1 0.2 + - - -
98D VAL* 3.2 8.3 + - - +
99D SER* 2.9 33.3 + - - -
102D TYR* 4.5 4.7 - - + -
119D LEU* 5.9 1.8 - - + -
135D ALA* 4.0 20.4 - - + -
138D MET* 4.0 21.5 - - + -
139D LEU* 4.2 19.5 - - + -
6H LEU* 3.6 30.5 - - + -
7H LEU* 4.3 15.5 - - + +
8H LYS 6.0 0.2 - - - +
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Residues in contact with LYS 96 (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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103C LEU* 5.6 7.7 - - - +
56D GLN* 4.7 2.5 - - - +
92D ASN* 2.8 27.4 + - - +
93D GLU* 3.3 39.2 + - - +
94D LEU 3.3 0.2 - - - -
95D ILE* 1.3 76.0 - - - +
97D VAL* 1.3 62.4 + - - +
99D SER 3.9 0.5 + - - -
102D TYR* 3.5 25.1 - - + +
103D LEU* 3.1 38.8 + - + +
104D GLY 3.5 1.9 + - - -
7H LEU* 3.4 28.7 - - + -
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Residues in contact with VAL 97 (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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55D ILE* 4.4 13.9 - - + +
56D GLN* 3.5 31.9 - - + +
93D GLU 3.2 16.6 - - - +
94D LEU* 3.1 9.1 + - - +
96D LYS* 1.3 78.6 - - - +
98D VAL* 1.3 56.9 + - - +
103D LEU* 4.3 8.3 - - + -
104D GLY* 3.3 18.2 - - - -
107D THR* 3.4 36.3 + - + +
111D VAL* 4.1 6.1 - - + -
112D LYS* 3.6 2.2 - - + +
115D ILE* 3.6 22.9 - - + -
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Residues in contact with VAL 98 (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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94D LEU 3.4 13.5 - - - +
95D ILE* 3.6 10.1 - - - +
97D VAL* 1.3 76.6 - - - +
99D SER* 1.3 61.4 + - - +
100D PRO* 3.9 3.3 - - - +
104D GLY* 4.1 0.8 - - - -
112D LYS* 3.5 56.9 + - + +
115D ILE* 3.8 22.9 - - + -
116D LEU* 4.2 12.6 - - + -
139D LEU* 4.1 23.8 - - + -
144D ILE* 3.3 21.2 - - + +
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Residues in contact with SER 99 (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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95D ILE* 2.9 23.6 + - - -
97D VAL 3.6 1.4 - - - -
98D VAL* 1.3 79.9 - - - +
100D PRO* 1.3 73.1 - - - +
101D LYS* 3.4 17.8 + - - +
102D TYR* 2.9 33.1 + - - +
104D GLY* 3.0 14.4 + - - -
138D MET* 6.2 0.2 - - - -
142D GLN* 4.6 2.9 + - - -
144D ILE* 3.6 17.6 - - - +
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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