Contacts of the helix formed by residues 108 - 121 (chain D) in PDB entry 2P80
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 PRO 108 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115C ASN* 3.2 44.9 - - + +
116C PRO 4.6 3.6 - - - +
118C GLU* 6.3 2.2 - - - -
82D TYR* 3.0 35.9 - - + +
107D LYS* 1.3 87.1 - - + +
109D LYS* 1.3 65.6 + - - +
110D ILE* 4.0 6.5 - - + -
111D VAL* 3.0 18.3 + - + +
112D GLN* 2.9 19.9 + - - +
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Residues in contact with LYS 109 (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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89C GLU* 1.9 86.7 + - + +
90C THR* 2.5 11.9 - - - +
91C ASN 4.6 0.7 - - - +
116C PRO* 3.0 30.8 + - + +
117C GLY* 5.6 0.2 - - - -
107D LYS 3.5 2.5 + - - -
108D PRO* 1.3 71.8 - - - +
110D ILE* 1.3 61.5 + - - +
112D GLN* 3.2 9.4 + - + +
113D GLU* 3.0 42.6 + - + +
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Residues in contact with ILE 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C THR* 2.4 48.7 - - - +
93C LEU* 4.6 2.7 - - + -
116C PRO* 3.6 13.1 - - + +
83D ALA 3.1 28.5 - - - +
84D MET 3.7 17.7 - - - +
85D GLY* 3.8 8.7 - - - +
108D PRO* 4.0 6.1 - - + -
109D LYS* 1.3 75.5 - - - +
111D VAL* 1.3 72.5 + - - +
113D GLU* 3.3 9.5 + - + +
114D ARG* 3.1 34.0 + - + +
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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
----------------------------------------------------------
75D LEU* 4.7 4.9 - - + -
82D TYR* 3.3 56.1 - - + +
85D GLY* 4.1 11.7 - - - -
87D ILE* 4.0 19.5 - - + +
107D LYS* 3.8 19.1 - - + -
108D PRO* 3.0 24.8 + - + +
110D ILE* 1.3 78.5 - - + +
112D GLN* 1.3 58.3 + - - +
114D ARG* 3.1 5.3 + - - +
115D LEU* 2.9 27.6 + - + +
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Residues in contact with GLN 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D VAL* 3.1 31.2 + - - +
105D ALA 4.4 0.5 - - - +
107D LYS* 2.9 41.0 + - + +
108D PRO 2.9 11.2 + - - +
109D LYS* 3.5 14.8 - - + +
111D VAL* 1.3 75.8 - - - +
113D GLU* 1.3 63.4 + - + +
115D LEU* 3.3 8.1 + - - +
116D GLU* 2.9 53.1 + - - +
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Residues in contact with GLU 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C GLU 4.4 0.2 - - - +
90C THR 4.9 1.7 - - - +
91C ASN 4.2 8.8 - - - +
92C THR* 3.6 25.1 - - - +
109D LYS* 3.0 39.1 + - + +
110D ILE* 3.6 12.7 - - + +
112D GLN* 1.3 76.7 - - + +
114D ARG* 1.3 64.7 + - + +
116D GLU* 3.5 11.3 + - - +
117D LYS* 3.2 21.5 + - - +
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Residues in contact with ARG 114 (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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93C LEU* 5.3 2.0 - - - +
13D GLU* 3.7 32.0 + - + +
14D GLY* 4.4 1.2 - - - +
15D ALA 2.9 20.6 + - - -
16D MET 3.1 13.0 + - - -
17D VAL* 3.1 26.5 - - - +
84D MET 2.8 27.7 + - - -
85D GLY* 2.8 27.9 + - - +
87D ILE* 4.5 7.4 - - + -
110D ILE* 3.1 23.9 + - + +
111D VAL 3.1 8.2 + - - +
113D GLU* 1.3 73.9 - - + +
115D LEU* 1.3 60.3 + - - +
117D LYS* 3.2 6.7 + - + +
118D VAL* 2.9 39.5 + - + +
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Residues in contact with LEU 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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75D LEU* 4.1 23.6 - - + -
87D ILE* 4.1 10.6 - - + +
89D LEU* 4.5 10.3 - - + -
99D LEU* 5.9 0.2 - - + -
102D ILE* 4.3 8.7 - - + +
103D VAL* 4.1 29.6 - - + -
107D LYS* 4.2 21.3 - - + +
111D VAL* 2.9 15.8 + - + +
112D GLN* 3.5 11.9 - - - +
114D ARG* 1.3 76.1 - - - +
116D GLU* 1.3 64.0 + - + +
118D VAL* 2.6 34.4 - - + +
119D ILE* 2.9 26.1 + - + +
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Residues in contact with GLU 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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103D VAL* 5.2 8.2 - - + +
112D GLN* 2.9 48.8 + - - +
113D GLU* 3.8 12.1 - - - +
115D LEU* 1.3 77.3 - - + +
117D LYS* 1.3 63.9 + - - +
119D ILE* 3.5 7.0 + - + +
120D ALA* 3.1 24.4 + - - +
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Residues in contact with LYS 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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13D GLU* 3.3 39.5 + - - +
113D GLU 3.2 10.3 + - - +
114D ARG* 3.2 12.4 + - - +
116D GLU* 1.3 80.1 - - - +
118D VAL* 1.3 58.6 + - + +
120D ALA* 3.0 3.6 + - - -
121D SER* 2.4 68.5 + - - +
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Residues in contact with VAL 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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13D GLU* 6.1 4.7 - - + -
21D ALA* 3.8 36.3 - - + +
22D TYR* 4.5 5.5 - - + +
87D ILE* 5.3 5.2 - - + -
89D LEU* 5.0 6.5 - - + -
114D ARG* 2.9 21.8 + - + +
115D LEU* 2.6 46.7 - - + +
117D LYS* 1.3 77.7 - - + +
119D ILE* 1.3 65.4 + - + +
121D SER 4.0 0.7 - - - +
122D ALA* 2.8 36.1 + - + +
123D LYS* 3.1 9.0 + - - -
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Residues in contact with ILE 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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22D TYR* 5.4 3.6 - - + -
89D LEU* 4.2 16.4 - - + -
99D LEU* 4.4 19.3 - - + -
103D VAL* 3.5 33.7 - - + -
115D LEU* 2.9 39.8 + - + +
116D GLU* 3.9 7.2 - - + +
118D VAL* 1.3 78.5 - - - +
120D ALA* 1.3 61.2 + - - +
123D LYS* 3.3 23.0 - - + +
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Residues in contact with ALA 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 GLU 3.1 16.6 + - - +
117D LYS* 3.0 3.7 + - - +
119D ILE* 1.3 83.3 - - - +
121D SER* 1.3 60.8 + - - +
122D ALA 3.7 0.8 + - - -
123D LYS* 3.8 21.5 + - - +
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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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13D GLU* 5.3 0.9 - - - +
117D LYS* 2.4 66.8 + - - +
118D VAL* 4.0 1.4 - - - +
120D ALA* 1.3 73.3 - - - +
122D ALA* 1.3 64.2 + - - +
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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