Contacts of the helix formed by residues 107 - 121 (chain B) in PDB entry 2PG0
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 THR 107 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105B TYR 3.8 2.0 + - - +
106B GLY* 1.3 77.5 - - - -
108B GLU* 1.3 65.8 + - - +
109B GLU* 3.1 17.2 + - - +
110B GLN* 3.0 37.5 + - - +
111B LYS* 3.1 19.4 + - - +
230B LEU 5.9 0.9 - - - +
232B GLY 6.3 0.9 - - - +
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Residues in contact with GLU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B LYS* 4.2 11.3 + - - -
64B TYR* 3.8 12.3 + - - -
106B GLY 5.1 0.5 - - - +
107B THR* 1.3 74.3 - - - +
109B GLU* 1.3 65.7 + - - +
111B LYS* 3.2 33.6 + - - +
112B GLN* 3.1 28.6 + - - +
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Residues in contact with GLU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B THR* 3.0 13.5 - - - +
108B GLU* 1.3 89.6 + - + +
110B GLN* 1.3 60.5 + - + +
112B GLN* 3.6 6.8 + - - +
113B LYS* 3.1 27.5 + - - +
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Residues in contact with GLN 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B ILE* 4.7 0.7 - - + -
105B TYR 4.5 0.7 - - - +
106B GLY* 3.4 12.2 - - - -
107B THR* 3.0 42.1 + - - +
109B GLU* 1.3 73.7 - - + +
111B LYS* 1.3 56.6 + - - +
113B LYS* 3.1 8.9 + - + +
114B TRP* 2.8 73.9 + - + +
228B TYR 2.8 29.6 + - - +
229B ASN 4.0 0.4 - - - -
230B LEU 2.9 26.2 + - - +
231B LEU* 4.1 5.3 - - - +
232B GLY 5.2 0.5 + - - -
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Residues in contact with LYS 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B TYR* 3.6 25.3 + - + +
102B ILE* 3.5 22.0 - - - +
103B ALA* 3.8 28.3 + - - +
106B GLY 3.6 15.7 + - - +
107B THR 3.1 15.1 + - - +
108B GLU* 3.2 37.7 + - - +
110B GLN* 1.3 75.4 - - - +
112B GLN* 1.3 58.8 + - - +
115B LEU* 2.8 46.8 + - + +
116B PRO* 3.2 5.0 - - - +
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Residues in contact with GLN 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B LYS* 4.9 9.1 + - - +
64B TYR* 3.6 22.6 - - + -
108B GLU 3.1 16.4 + - - +
109B GLU* 3.8 7.2 - - - +
111B LYS* 1.3 78.4 - - - +
113B LYS* 1.3 61.2 + - - +
116B PRO* 3.3 29.3 - - - +
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Residues in contact with LYS 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B GLU 3.1 17.6 + - - +
110B GLN* 3.1 9.1 + - + +
112B GLN* 1.3 78.1 - - - +
114B TRP* 1.3 89.6 + - + +
116B PRO* 4.4 1.1 - - - +
117B LYS* 4.5 19.6 - - - +
193B GLU* 4.0 16.0 + - - -
228B TYR* 3.9 28.9 + - - -
229B ASN* 4.7 3.0 + - - -
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Residues in contact with TRP 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B ILE* 4.2 27.1 - - + -
110B GLN* 2.8 60.2 + - + +
113B LYS* 1.3 101.7 - - + +
115B LEU* 1.3 65.7 + - - +
116B PRO* 3.4 2.7 - - - -
117B LYS* 3.2 7.7 + - - +
118B CYS* 3.1 23.3 + - - -
123B LEU* 4.0 9.7 - - + +
169B LEU* 3.7 32.6 - - + +
191B VAL* 3.8 38.1 - - + -
193B GLU* 3.4 23.3 + - - -
228B TYR 4.8 0.2 - - - -
229B ASN* 3.7 24.9 - - - -
231B LEU* 5.1 2.7 - - + -
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Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B TRP* 4.8 0.2 - - + -
60B VAL* 4.4 21.5 - - + -
64B TYR* 4.0 28.3 - - + -
99B THR* 4.1 19.5 - - - +
102B ILE* 3.8 31.4 - - + -
103B ALA* 4.1 15.7 - - + +
111B LYS* 2.8 48.0 + - + +
114B TRP* 1.3 73.6 - - - +
116B PRO* 1.4 62.2 - - + +
118B CYS* 3.2 6.7 + - + +
119B VAL* 3.1 27.6 + - - +
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Residues in contact with PRO 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B TYR* 3.2 38.2 - - + +
111B LYS 3.2 13.2 - - - +
112B GLN* 3.3 26.7 - - - +
113B LYS 4.4 1.6 - - - +
114B TRP 3.5 2.9 - - - +
115B LEU* 1.4 92.5 - - + +
117B LYS* 1.3 59.1 + - + +
119B VAL* 3.3 4.9 + - - +
120B THR* 3.2 31.0 + - + +
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Residues in contact with LYS 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B LYS 4.5 12.8 - - - +
114B TRP 3.2 4.0 + - - +
116B PRO* 1.3 79.3 - - + +
118B CYS* 1.3 61.0 + - - +
120B THR* 3.4 8.3 - - - +
121B GLY 3.0 20.6 + - - -
122B GLU* 2.9 58.2 + - + +
123B LEU* 3.2 39.9 + - + -
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Residues in contact with CYS 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B LEU* 3.8 6.2 - - - +
57B CYS* 3.8 6.4 - - - -
94B HIS* 2.8 28.7 + - + -
99B THR* 3.8 26.0 - - + -
102B ILE* 4.5 6.5 - - - -
114B TRP 3.1 21.9 + - - -
115B LEU* 3.2 11.8 + - + +
117B LYS* 1.3 74.7 - - - +
119B VAL* 1.3 64.5 + - - +
121B GLY 3.5 6.6 + - - -
123B LEU* 3.7 11.0 - - - -
125B THR* 3.8 19.1 - - - -
169B LEU* 4.4 11.7 - - - -
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Residues in contact with VAL 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B GLY* 3.5 14.5 - - - +
54B GLY* 5.6 4.0 - - - -
56B LEU* 3.4 31.3 - - - +
57B CYS* 4.1 6.3 - - + +
60B VAL* 3.8 37.0 - - + -
64B TYR 4.5 2.2 - - - +
65B GLY* 3.3 26.5 - - - +
66B GLY* 4.2 7.6 - - - +
115B LEU 3.1 15.3 + - - +
116B PRO 3.3 8.9 + - - +
118B CYS* 1.3 77.0 - - - +
120B THR* 1.3 63.2 + - + +
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Residues in contact with THR 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B TRP 4.3 1.4 - - - +
48B ALA* 4.2 9.5 - - - +
51B GLY* 3.3 25.3 + - - +
52B GLU* 4.3 0.6 + - - -
116B PRO 3.2 13.9 + - - +
117B LYS* 3.1 20.3 + - - +
119B VAL* 1.3 80.2 - - + +
121B GLY* 1.3 60.2 + - - +
122B GLU* 3.3 14.6 + - - +
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Residues in contact with GLY 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ARG* 3.9 15.4 + - - +
47B TRP* 4.7 9.8 - - - +
48B ALA* 5.4 2.2 + - - -
56B LEU* 3.5 20.4 - - - -
94B HIS* 5.3 0.2 - - - -
117B LYS 3.0 6.6 + - - -
118B CYS 3.5 3.7 + - - -
119B VAL 3.4 3.2 - - - -
120B THR* 1.3 78.5 - - - +
122B GLU* 1.3 63.6 + - - +
123B LEU 3.2 8.0 + - - -
124B ILE* 4.1 10.9 - - - +
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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
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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