Contacts of the helix formed by residues 95 - 110 (chain A) in PDB entry 2PGE
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 ASP 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A PHE 5.4 0.2 - - - -
94A SER* 1.3 81.2 + - - +
96A TYR* 1.3 65.7 + - - +
97A ARG* 4.1 17.1 - - + +
98A SER* 3.1 16.3 + - - +
99A VAL* 3.1 19.9 + - - +
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Residues in contact with TYR 96 (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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91A ALA* 5.0 15.9 - - + +
94A SER 3.8 4.2 + - - -
95A ASP* 1.3 74.8 - - - +
97A ARG* 1.3 60.2 + - + +
99A VAL* 3.6 21.8 - - + +
100A LEU* 2.9 36.8 + - + +
130A LEU* 5.0 2.7 - - + -
133A LEU* 5.7 4.5 - - + -
134A SER* 5.9 2.4 - - - -
139A GLU 5.3 0.9 + - - -
140A TRP 4.0 9.2 + - - -
141A PHE* 3.4 45.6 - + + -
142A ALA* 3.2 38.2 + - - +
336A LEU* 3.8 22.9 - - + -
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Residues in contact with ARG 97 (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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95A ASP* 3.1 11.1 - - + +
96A TYR* 1.3 80.6 - - + +
98A SER* 1.3 58.6 + - - +
100A LEU* 3.5 9.7 + - + +
101A THR* 2.9 31.3 + - - -
299A HIS* 4.9 0.9 + - - -
306A GLU* 3.9 16.9 + - - +
309A ARG* 3.5 25.9 - - - +
337A TYR* 3.6 29.1 + - - +
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Residues in contact with SER 98 (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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88A ARG* 3.2 28.6 + - - -
94A SER* 4.3 5.6 - - - -
95A ASP* 3.1 21.3 + - - +
97A ARG* 1.3 77.7 - - - +
99A VAL* 1.3 65.4 + - - +
101A THR* 3.2 8.4 + - - -
102A ASP* 3.0 25.9 + - - +
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Residues in contact with VAL 99 (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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84A PHE* 4.0 5.2 - - + -
88A ARG* 4.3 16.4 - - + +
91A ALA* 5.7 4.0 - - + -
94A SER* 4.0 17.5 - - - +
95A ASP 3.1 15.3 + - - +
96A TYR* 3.6 22.2 - - + +
98A SER* 1.3 76.8 - - - +
100A LEU* 1.3 56.8 + - - +
102A ASP* 3.2 10.3 + - - +
103A ILE* 2.9 43.3 + - + +
130A LEU* 4.1 11.9 - - + -
133A LEU* 3.8 25.6 - - + -
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Residues in contact with LEU 100 (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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96A TYR* 2.9 25.9 + - + +
97A ARG* 3.8 7.9 - - + +
98A SER 3.3 0.2 - - - -
99A VAL* 1.3 76.5 - - - +
101A THR* 1.3 57.5 + - - +
103A ILE* 3.4 5.6 + - + +
104A ALA* 2.9 27.7 + - - +
126A GLU* 3.8 30.2 - - + +
130A LEU* 4.0 26.0 - - + -
141A PHE* 4.3 11.9 - - + -
298A PHE* 3.8 31.9 - - + +
299A HIS* 3.8 19.5 + - + +
302A GLY* 6.3 0.2 - - - -
333A TRP* 4.3 11.0 - - + +
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Residues in contact with THR 101 (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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97A ARG 2.9 19.2 + - - -
98A SER* 3.5 12.0 - - - -
99A VAL 3.2 0.4 - - - -
100A LEU* 1.3 78.9 - - - +
102A ASP* 1.3 66.5 + - - +
104A ALA* 3.2 5.2 + - + +
105A GLY* 3.1 17.7 + - - -
299A HIS* 3.7 22.6 + - + -
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Residues in contact with ASP 102 (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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80A ARG* 4.8 3.0 + - - +
84A PHE* 3.6 19.7 - - + -
87A GLU* 5.2 2.9 - - - +
88A ARG* 2.6 45.9 + - - +
98A SER* 3.0 15.8 + - - +
99A VAL 3.6 7.4 - - - +
101A THR* 1.3 81.0 - - - +
103A ILE* 1.3 64.3 + - - +
105A GLY* 3.1 12.2 + - - +
106A ILE* 3.1 18.3 + - - +
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Residues in contact with ILE 103 (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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84A PHE* 3.6 21.5 - - + -
99A VAL* 2.9 25.7 + - + +
100A LEU* 3.7 9.2 - - + +
101A THR 3.2 0.2 - - - -
102A ASP* 1.3 77.4 - - - +
104A ALA* 1.3 63.3 + - - +
106A ILE* 3.0 9.9 + - - +
107A LEU* 2.9 34.3 + - + +
126A GLU* 4.1 14.1 - - + -
129A LEU* 3.6 36.1 - - + -
130A LEU* 3.6 40.4 - - + +
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Residues in contact with ALA 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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100A LEU 2.9 14.6 + - - +
101A THR* 3.2 9.2 + - + +
103A ILE* 1.3 76.7 - - - +
105A GLY* 1.3 57.8 - - - +
107A LEU* 4.4 4.7 - - - -
108A ASP* 2.9 37.7 + - - +
122A ARG* 3.3 22.4 + - - +
299A HIS* 3.6 27.8 - - + +
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Residues in contact with GLY 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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80A ARG* 3.3 33.9 + - - -
101A THR 3.1 9.4 + - - -
102A ASP* 3.1 7.3 + - - -
104A ALA* 1.3 78.5 - - - +
106A ILE* 1.3 61.7 + - - +
108A ASP* 3.4 9.8 + - - +
109A SER* 3.1 17.5 + - - -
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Residues in contact with ILE 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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80A ARG* 4.2 21.3 - - + +
81A LEU* 3.9 22.0 - - + +
84A PHE* 3.8 39.0 - - + -
102A ASP* 3.1 13.2 + - + +
103A ILE* 3.0 11.7 + - - +
105A GLY* 1.3 75.0 - - - +
107A LEU* 1.3 59.9 - - - +
109A SER* 2.6 25.1 + - - +
110A TRP* 2.9 51.9 + - + +
129A LEU* 4.2 8.5 - - + -
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Residues in contact with LEU 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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103A ILE* 2.9 36.7 + - + +
104A ALA* 3.8 1.8 - - - +
106A ILE* 1.3 75.6 - - - +
108A ASP* 1.3 60.2 + - - +
110A TRP* 3.2 15.8 + - + +
111A GLN 3.2 3.6 + - - -
112A VAL* 2.9 36.1 + - + +
122A ARG* 3.6 54.1 - - + +
125A LEU* 3.6 26.5 - - + -
126A GLU* 4.1 10.8 - - + +
129A LEU* 3.8 16.6 - - + -
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Residues in contact with ASP 108 (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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104A ALA* 2.9 24.6 + - - +
105A GLY* 3.5 8.8 - - - +
107A LEU* 1.3 76.7 - - - +
109A SER* 1.3 58.8 + - - +
111A GLN* 2.9 29.8 + - - +
114A THR* 3.7 17.4 - - + +
122A ARG* 2.8 28.3 + - - -
300A TYR* 4.7 1.6 + - - -
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Residues in contact with SER 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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72A ARG* 4.6 8.0 + - - -
76A GLU* 5.3 4.5 + - - +
80A ARG* 4.2 19.7 - - - +
105A GLY 3.1 12.9 + - - -
106A ILE* 2.6 24.9 + - - +
108A ASP* 1.3 77.7 - - - +
110A TRP* 1.3 70.2 + - - +
111A GLN* 3.1 8.6 + - - +
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Residues in contact with TRP 110 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A MET* 4.1 6.9 - - + -
37A LEU* 4.1 18.6 - - + -
69A LEU* 3.8 24.7 - - + +
72A ARG* 3.7 17.5 + - - +
73A LEU* 3.5 42.4 - - + +
76A GLU* 3.9 19.0 + - - -
78A PRO* 6.1 0.2 - - + -
81A LEU* 4.0 22.1 - - + +
106A ILE* 2.9 29.8 + - + +
107A LEU* 3.7 23.1 - - + +
108A ASP 3.1 0.8 - - - -
109A SER* 1.3 87.0 + - - +
111A GLN* 1.3 71.7 + - - +
112A VAL* 3.2 7.3 + - + +
125A LEU* 4.6 3.8 - - + -
129A LEU* 3.8 36.1 - - + -
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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