Contacts of the helix formed by residues 103 - 116 (chain A) in PDB entry 2PPL
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 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A ASP* 3.3 3.5 + - - +
102A GLU* 1.3 80.9 - - - +
104A TRP* 1.3 58.9 + - - +
105A VAL* 3.2 3.1 - - - +
106A THR* 3.4 20.5 - - - +
107A ASP* 2.9 38.6 + - - -
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Residues in contact with TRP 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A ILE* 3.8 24.5 - - + -
93A ILE 4.5 3.6 - - - -
94A HIS* 4.2 14.8 - - - +
96A PHE 4.9 5.9 + - - -
97A ILE* 5.0 7.0 - - + +
101A ASP* 3.6 22.7 + - - +
102A GLU* 3.5 5.3 - - - -
103A SER* 1.3 77.7 - - - +
105A VAL* 1.3 79.7 + - + +
107A ASP* 3.4 12.4 - - - +
108A MET* 2.8 46.8 + - + +
168A ILE* 5.5 0.9 - - + -
170A HIS* 3.6 39.8 + + + -
193A LEU* 4.7 5.2 - - + -
285A TYR* 3.5 67.6 - + + -
289A LEU* 4.6 6.3 - - + +
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Residues in contact with VAL 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A ILE* 3.7 22.8 - - + +
94A HIS* 4.5 14.6 - - + +
102A GLU 5.3 5.6 - - - +
103A SER* 3.2 1.4 - - - +
104A TRP* 1.3 117.2 - - + +
106A THR* 1.3 57.9 + - - +
108A MET* 3.1 6.5 + - - +
109A CYS* 3.1 25.3 + - - -
122A CYS* 3.2 37.2 - - + -
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Residues in contact with THR 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A TYR* 4.2 32.3 - - - +
64A PRO 4.6 1.6 + - - -
65A ASN 5.1 1.6 + - - -
103A SER* 3.4 30.7 - - - +
105A VAL* 1.3 76.8 - - + +
107A ASP* 1.3 64.2 + - - +
108A MET 3.2 0.7 - - - -
109A CYS* 3.4 10.7 + - - +
110A LYS* 3.1 47.0 + - - +
122A CYS* 4.8 0.9 - - - -
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Residues in contact with ASP 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A ASP* 4.6 5.7 - - - +
103A SER* 2.9 34.2 + - - +
104A TRP* 3.4 11.1 + - - +
105A VAL 3.3 0.2 - - - -
106A THR* 1.3 78.0 - - - +
108A MET* 1.3 58.2 + - - +
110A LYS* 3.4 14.3 + - - +
111A LYS* 3.0 34.3 + - - +
289A LEU* 4.0 12.3 - - + +
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Residues in contact with MET 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ILE* 3.8 21.8 - - + -
104A TRP* 2.8 35.8 + - + +
105A VAL* 3.1 11.2 + - - +
107A ASP* 1.3 74.8 - - - +
109A CYS* 1.3 65.8 + - - +
111A LYS* 3.2 2.4 + - - +
112A LEU* 2.9 27.8 + - + +
168A ILE* 4.2 13.2 - - - -
193A LEU* 4.8 1.6 - - + -
285A TYR* 3.9 10.5 - - + +
288A TYR* 3.6 35.7 - - + -
289A LEU* 3.6 33.4 - - + +
292A ILE* 4.3 9.0 - - + -
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Residues in contact with CYS 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A TYR* 4.0 12.6 - - + -
64A PRO 5.5 0.2 - - - +
92A ILE* 4.2 0.4 - - - -
105A VAL 3.1 11.5 + - - -
106A THR* 3.6 10.5 - - - +
107A ASP 3.4 0.2 - - - -
108A MET* 1.3 74.4 - - - +
110A LYS* 1.3 58.1 + - + +
112A LEU* 2.9 21.9 + - - +
113A PHE* 2.9 28.6 + - + -
120A CYS* 2.0 54.0 - - + -
122A CYS* 3.5 28.3 - - - -
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Residues in contact with LYS 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A PRO* 4.1 18.1 + - + +
65A ASN* 3.6 28.6 + - - +
106A THR* 3.1 45.3 + - - +
107A ASP* 3.9 12.8 + - - +
108A MET 3.3 0.2 - - - -
109A CYS* 1.3 77.9 - - + +
111A LYS* 1.3 61.8 + - - +
113A PHE* 3.3 23.2 + - + +
114A GLU* 3.4 17.2 + - - +
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Residues in contact with LYS 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ASP* 3.0 18.3 + - - +
108A MET 3.5 9.2 - - - +
110A LYS* 1.3 77.8 - - - +
112A LEU* 1.3 61.2 + - - +
114A GLU* 3.2 32.2 + - - +
115A VAL 3.9 0.3 + - - -
289A LEU* 3.9 43.3 - - + +
290A GLU* 5.5 2.0 - - - +
292A ILE* 3.6 24.3 - - + +
293A LEU* 4.1 26.6 - - + +
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Residues in contact with LEU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ARG* 3.9 22.2 - - + +
92A ILE* 4.4 13.5 - - + -
108A MET* 2.9 27.4 + - + +
109A CYS 2.9 6.7 + - - +
111A LYS* 1.3 77.4 - - - +
113A PHE* 1.3 58.6 + - - +
114A GLU 3.0 0.2 - - - -
115A VAL* 3.0 7.1 + - + +
116A GLU* 3.0 47.2 + - + +
118A VAL* 4.1 10.1 - - + -
120A CYS* 4.4 10.5 - - + -
168A ILE* 4.9 2.9 - - + -
288A TYR* 5.1 1.3 - - + -
292A ILE* 3.6 21.1 - - + -
327A HIS* 3.3 36.3 - - + +
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Residues in contact with PHE 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A TYR* 3.6 21.3 - - + -
60A THR 3.4 26.7 - - - -
61A ASN* 3.6 32.8 + - - +
64A PRO* 3.6 33.9 - - + -
109A CYS* 2.9 26.3 + - + -
110A LYS* 3.7 15.3 - - + +
111A LYS 3.3 0.6 - - - -
112A LEU* 1.3 75.0 - - - +
114A GLU* 1.3 60.8 + - - +
115A VAL 3.2 0.6 + - - -
116A GLU 3.5 7.7 + - - +
118A VAL* 3.6 34.5 - - + -
120A CYS* 4.0 9.0 - - + -
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Residues in contact with GLU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A LYS 3.4 11.2 + - - +
111A LYS* 3.2 26.6 + - - +
112A LEU 3.0 1.0 - - - -
113A PHE* 1.3 79.5 - - - +
115A VAL* 1.3 59.1 + - - +
293A LEU* 3.8 36.8 - - + +
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Residues in contact with VAL 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A LEU* 3.0 14.7 + - - +
114A GLU* 1.3 83.0 - - - +
116A GLU* 1.3 68.7 + - + +
292A ILE* 3.7 37.9 - - + +
293A LEU* 3.8 20.4 - - + -
327A HIS* 4.7 8.3 - - - +
328A TYR* 4.2 12.8 - - - +
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Residues in contact with GLU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ASN* 2.9 18.9 + - - -
88A LYS* 5.7 2.5 - - - +
90A ARG* 2.8 45.5 + - - -
112A LEU* 3.0 34.5 + - - +
113A PHE* 3.5 4.4 + - - +
114A GLU 3.7 0.6 - - - -
115A VAL* 1.3 86.7 - - + +
117A GLU* 1.3 65.2 + - - +
118A VAL* 3.4 27.2 + - + +
327A HIS* 4.4 6.2 + - - -
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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