Contacts of the helix formed by residues 108 - 126 (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 SER 108 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D GLU* 3.0 32.5 + - - +
106D ARG 4.2 0.8 + - - -
107D THR* 1.3 76.8 - - - +
109D GLU* 1.3 67.0 + - - +
110D LYS 4.2 1.1 - - - -
111D VAL* 3.0 26.5 + - - +
112D LYS* 3.0 18.8 + - - +
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Residues in contact with GLU 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D THR 3.6 2.9 + - - -
108D SER* 1.3 71.3 - - - +
110D LYS* 1.3 57.0 + - - +
112D LYS* 4.6 12.1 - - - +
113D ASN* 2.8 56.0 + - - +
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Residues in contact with LYS 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D GLU* 3.5 25.6 + - - +
64D ILE* 3.5 28.5 - - + -
108D SER* 3.1 1.6 + - - -
109D GLU* 1.3 80.0 - - - +
111D VAL* 1.3 62.1 + - - +
113D ASN* 3.9 4.1 - - - +
114D LYS* 3.0 25.7 + - + +
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Residues in contact with VAL 111 (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 11.7 - - - +
60D GLU* 3.8 9.0 - - + -
63D ALA* 4.1 14.1 - - + -
64D ILE* 3.8 25.1 - - + +
67D LEU* 4.0 15.3 - - + -
97D VAL* 4.1 4.0 - - + -
107D THR* 3.8 17.9 - - + -
108D SER* 3.0 21.4 + - - +
110D LYS* 1.3 77.2 - - - +
112D LYS* 1.3 63.5 - - - +
114D LYS* 3.2 7.6 + - - +
115D ILE* 3.1 33.3 + - + +
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Residues in contact with LYS 112 (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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97D VAL 3.6 19.5 - - - +
98D VAL* 3.5 40.6 + - + +
100D PRO* 6.0 2.8 - - - +
104D GLY* 3.0 28.3 + - - +
105D SER* 4.8 2.0 - - - +
107D THR* 3.5 23.3 + - + -
108D SER 3.0 9.1 + - - +
109D GLU* 3.9 11.9 - - - +
111D VAL* 1.3 77.0 - - - +
113D ASN* 1.3 66.8 + - - +
115D ILE* 3.2 4.9 + - - +
116D LEU* 3.0 28.6 + - + +
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Residues in contact with ASN 113 (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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109D GLU* 2.8 47.4 + - - +
110D LYS* 4.0 3.9 - - - +
112D LYS* 1.3 74.8 - - - +
114D LYS* 1.3 62.5 + - - +
116D LEU* 3.1 18.1 + - - +
117D GLU* 3.0 31.4 + - + +
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Residues in contact with LYS 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D ILE* 5.7 7.0 - - + +
67D LEU* 3.6 30.7 - - + -
68D THR* 5.1 5.3 + - - +
71D GLU* 2.5 40.7 + - - -
110D LYS* 3.0 20.0 + - + +
111D VAL* 3.5 5.8 - - - +
113D ASN* 1.3 78.1 - - - +
115D ILE* 1.3 61.8 + - - +
117D GLU* 3.2 23.7 + - - +
118D LEU* 3.1 37.1 + - + +
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Residues in contact with ILE 115 (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* 3.9 17.7 - - + -
67D LEU* 3.5 20.4 - - + -
94D LEU* 4.0 25.8 - - + +
97D VAL* 3.6 36.8 - - + -
98D VAL* 3.8 16.2 - - + -
111D VAL* 3.1 16.7 + - + +
112D LYS 3.6 6.3 - - - +
114D LYS* 1.3 75.5 - - - +
116D LEU* 1.3 59.0 + - - +
118D LEU* 3.2 9.3 + - + +
119D LEU* 2.9 47.0 + - + +
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Residues in contact with LEU 116 (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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98D VAL* 4.2 17.7 - - + -
112D LYS* 3.0 21.2 + - + +
113D ASN* 3.1 20.6 + - - +
115D ILE* 1.3 75.7 - - - +
117D GLU* 1.3 61.8 + - - +
119D LEU* 4.1 7.2 - - + -
120D TYR* 3.4 20.1 + - - +
136D TYR* 4.0 7.6 - - + -
139D LEU* 4.0 19.7 - - + -
144D ILE* 3.5 28.7 - - + +
145D VAL* 3.8 27.6 - - + -
149D PRO* 4.3 11.4 - - + +
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Residues in contact with GLU 117 (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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113D ASN* 3.0 20.8 + - + +
114D LYS* 3.5 25.7 + - + +
115D ILE 3.2 0.2 - - - -
116D LEU* 1.3 77.0 - - - +
118D LEU* 1.3 63.0 + - + +
120D TYR* 3.2 5.9 + - - +
121D SER* 2.9 28.4 + - - -
149D PRO* 4.3 30.5 - - + +
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Residues in contact with LEU 118 (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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67D LEU* 4.2 31.6 - - + +
70D LEU* 4.3 14.4 - - + -
71D GLU* 3.5 44.6 - - + +
94D LEU* 6.4 0.4 - - + -
114D LYS* 3.1 28.6 + - - +
115D ILE* 3.2 8.0 + - + +
117D GLU* 1.3 76.4 - - + +
119D LEU* 1.3 67.2 + - - +
121D SER* 3.0 13.1 + - - +
122D TRP* 2.9 46.9 + - + +
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Residues in contact with LEU 119 (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* 4.3 13.5 - - + -
94D LEU* 4.0 17.3 - - + -
95D ILE* 5.9 2.0 - - + +
98D VAL* 5.3 0.4 - - + -
115D ILE* 2.9 38.7 + - + +
116D LEU* 4.1 8.3 - - + +
118D LEU* 1.3 76.3 - - - +
120D TYR* 1.3 61.9 + - - +
122D TRP* 3.3 26.7 + - + +
123D THR* 3.2 28.0 + - - +
132D ILE* 3.9 13.6 - - + +
135D ALA* 5.4 5.2 - - + -
136D TYR* 3.9 17.5 - - + +
139D LEU* 3.6 31.0 - - + -
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Residues in contact with TYR 120 (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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116D LEU 3.4 11.8 + - - +
117D GLU* 3.2 8.9 + - - +
118D LEU 3.1 0.6 - - - -
119D LEU* 1.3 76.7 - - - +
121D SER* 1.3 71.2 + - - +
122D TRP 2.9 0.9 + - - -
123D THR* 2.8 26.2 + - - -
124D VAL* 3.2 33.3 + - + +
136D TYR* 3.4 35.3 - + - +
148D ASP* 3.4 29.5 + - + +
149D PRO* 4.0 31.4 - - + -
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Residues in contact with SER 121 (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 LYS* 6.1 0.9 - - - -
117D GLU 2.9 16.3 + - - -
118D LEU* 3.0 21.5 + - - +
120D TYR* 1.3 79.3 - - - +
122D TRP* 1.3 68.0 + - - +
124D VAL* 3.5 5.1 + - - +
125D GLY* 2.9 25.6 + - - -
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Residues in contact with TRP 122 (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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70D LEU* 3.8 30.7 - - + -
71D GLU* 5.5 1.0 - - - +
74D MET* 3.5 49.5 - - + +
85D VAL* 3.9 18.8 - - + -
91D LEU* 4.9 1.1 - - + -
94D LEU* 3.9 20.9 - - + -
118D LEU* 2.9 43.1 + - + +
119D LEU* 3.7 24.5 - - + +
120D TYR 3.0 0.2 - - - -
121D SER* 1.3 84.4 + - - +
123D THR* 1.3 58.1 + - - +
124D VAL 2.9 4.7 - - - -
125D GLY* 4.3 0.7 - - - +
126D LEU* 2.6 46.5 + - + +
132D ILE* 3.8 29.2 - - + -
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Residues in contact with THR 123 (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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119D LEU 3.2 13.9 + - - +
120D TYR* 2.8 31.4 + - - -
122D TRP* 1.3 76.0 - - - +
124D VAL* 1.3 60.8 + - - +
126D LEU 4.9 3.4 - - - -
127D PRO* 3.9 20.9 - - - +
129D GLU 6.1 0.4 - - - -
132D ILE* 3.7 11.2 - - + -
133D ALA* 3.6 37.0 - - - +
136D TYR* 3.8 21.2 - - + -
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Residues in contact with VAL 124 (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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120D TYR* 3.2 49.5 + - + +
121D SER* 3.9 5.4 - - - +
122D TRP 2.9 1.6 - - - -
123D THR* 1.3 82.6 - - - +
125D GLY* 1.3 63.1 + - - +
126D LEU 3.4 0.9 - - - -
127D PRO* 3.5 10.6 - - - +
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Residues in contact with GLY 125 (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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121D SER 2.9 19.0 + - - -
124D VAL* 1.3 77.1 - - - +
126D LEU* 1.3 66.7 + - - +
127D PRO* 3.4 5.7 - - - +
128D GLU* 4.2 2.8 - - - +
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Residues in contact with LEU 126 (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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74D MET* 3.7 19.1 - - + +
82D HIS* 3.6 55.0 - - + +
122D TRP* 2.6 34.7 + - + +
123D THR* 4.9 0.5 - - - -
125D GLY* 1.3 79.3 - - - +
127D PRO* 1.3 61.5 - - - +
128D GLU* 2.9 32.2 + - + +
129D GLU* 3.0 29.5 + - + +
132D ILE* 5.0 0.9 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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