Contacts of the helix formed by residues 94 - 109 (chain A) in PDB entry 4PJW
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 ALA 94 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A SER* 1.3 79.7 - - - +
95A MSE 1.3 64.3 + - - +
96A GLN* 4.3 4.7 - - + +
97A SER* 3.5 34.8 + - - +
98A VAL* 3.7 9.0 + - - +
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Residues in contact with MSE 95 (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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87A VAL* 5.4 1.1 - - + +
88A VAL* 3.6 38.6 - - + +
93A SER 3.7 6.2 + - - +
94A ALA* 1.3 70.6 - - - +
96A GLN* 1.3 66.2 + - - +
97A SER 3.0 2.1 + - - -
98A VAL* 3.1 33.5 + - + +
99A VAL* 3.0 26.2 + - + +
174A SER* 3.6 29.8 - - - +
177A GLU* 3.6 23.1 - - + +
178A PHE* 3.5 37.2 - - + +
181A VAL* 4.9 4.0 - - + -
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Residues in contact with GLN 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ALA* 3.4 4.4 - - + +
95A MSE 1.3 78.6 - - - +
97A SER* 1.3 57.7 + - - +
99A VAL* 3.9 0.4 - - - -
100A ASP* 3.0 51.1 + - - +
181A VAL* 3.9 22.4 - - + +
185A GLN* 3.7 30.7 + - + +
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Residues in contact with SER 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A SER* 5.4 4.3 - - - -
94A ALA* 3.5 29.0 + - - +
95A MSE 3.0 0.6 - - - -
96A GLN* 1.3 80.1 - - - +
98A VAL* 1.3 55.5 + - - +
100A ASP* 3.6 4.5 + - - +
101A ASP* 2.9 37.7 + - - +
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Residues in contact with VAL 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 5.0 15.3 - - + -
87A VAL* 4.4 26.7 - - + -
88A VAL* 5.6 2.2 - - + -
93A SER* 5.7 1.6 - - - +
94A ALA 3.8 7.6 - - - +
95A MSE 3.1 44.0 - - + +
97A SER* 1.3 77.0 - - - +
99A VAL* 1.3 60.4 + - - +
101A ASP* 3.4 10.6 + - + +
102A TRP* 2.8 28.0 + - + +
178A PHE* 4.2 13.0 - - + -
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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
----------------------------------------------------------
95A MSE 3.0 19.9 + - - +
96A GLN 3.9 3.4 - - - +
98A VAL* 1.3 77.8 - - - +
100A ASP* 1.3 58.0 + - - +
102A TRP* 3.0 5.3 + - - +
103A ILE* 2.8 39.8 + - + +
178A PHE* 3.6 39.5 - - + +
181A VAL* 3.7 25.8 - - + +
182A LEU* 3.6 31.2 - - + +
185A GLN* 4.1 7.6 - - + -
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Residues in contact with ASP 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A GLN* 3.0 40.5 + - - +
97A SER* 3.8 5.4 - - - +
99A VAL* 1.3 77.2 - - - +
101A ASP* 1.3 59.9 + - - +
103A ILE* 3.4 11.2 + - - +
104A GLU* 2.9 32.1 + - - +
185A GLN* 3.0 28.8 + - - +
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Residues in contact with ASP 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A SER* 2.9 32.5 + - - +
98A VAL* 3.6 12.5 - - + +
99A VAL 3.2 0.2 - - - -
100A ASP* 1.3 77.6 - - - +
102A TRP* 1.3 62.0 + - - +
104A GLU* 3.1 31.2 - - - +
105A SER* 3.2 10.9 + - - -
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Residues in contact with TRP 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 4.2 27.8 - - + -
98A VAL* 2.8 19.4 + - + +
99A VAL* 3.4 6.5 - - - +
101A ASP* 1.3 75.2 - - - +
103A ILE* 1.3 68.7 + - + +
105A SER* 2.7 24.5 + - - -
106A TYR* 2.9 45.1 + + + -
113A ALA* 3.0 41.1 + - + +
114A LEU* 4.1 4.0 - - + -
116A ASP* 4.9 2.2 - - + -
117A LEU* 3.7 30.5 - - + +
178A PHE* 5.1 7.9 - + + -
182A LEU* 3.7 29.6 - - + -
186A CYS* 5.0 0.9 - - - -
190A ILE* 5.4 0.2 - - + -
196A MSE 3.9 26.0 - - + -
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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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99A VAL* 2.8 28.8 + - + +
100A ASP* 3.8 13.0 - - - +
102A TRP* 1.3 84.0 - - + +
104A GLU* 1.3 63.3 + - - +
106A TYR* 3.3 4.2 + - - +
107A LYS* 3.2 44.9 + - - +
185A GLN* 3.6 40.8 - - + +
186A CYS* 3.8 20.9 - - - -
190A ILE* 3.6 20.0 - - + -
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Residues in contact with GLU 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 ASP 2.9 15.9 + - - +
101A ASP* 3.1 25.0 - - - +
103A ILE* 1.3 79.4 - - - +
105A SER* 1.3 61.6 + - - +
107A LYS* 3.3 18.6 + - - +
108A HIS* 3.3 11.1 + - - +
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Residues in contact with SER 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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101A ASP 3.2 9.1 + - - -
102A TRP* 2.7 27.4 + - - -
104A GLU* 1.3 76.6 - - - +
106A TYR* 1.3 58.8 + - - +
108A HIS* 3.4 8.3 - - - +
109A ASP* 2.8 32.7 + - - +
112A ILE* 4.7 13.3 - - - +
113A ALA* 4.0 13.1 - - - +
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Residues in contact with TYR 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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102A TRP* 2.9 43.7 + + + +
103A ILE 3.3 5.6 + - - +
105A SER* 1.3 77.3 + - - +
107A LYS* 1.3 63.1 + - + +
109A ASP 4.1 0.4 - - - -
110A ARG* 3.2 68.9 + - + +
113A ALA* 3.7 7.8 - - + +
114A LEU* 4.0 18.4 - - + -
190A ILE* 3.6 34.8 - - + -
193A ASP* 2.4 33.1 + - - -
195A TYR* 3.8 3.1 - - - -
196A MSE 3.5 20.2 + - + +
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Residues in contact with LYS 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* 3.2 36.2 + - + +
104A GLU* 3.5 11.6 - - + +
105A SER 3.2 0.4 - - - -
106A TYR* 1.3 78.1 - - + +
108A HIS* 1.3 65.3 + - - +
110A ARG* 5.0 0.5 + - - +
189A SER* 6.0 2.0 - - - -
190A ILE* 4.7 13.0 - - + -
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Residues in contact with HIS 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 GLU 3.3 8.9 + - - +
105A SER* 3.2 12.5 + - - +
107A LYS* 1.3 82.4 - - - +
109A ASP* 1.3 72.8 + - + +
112A ILE* 5.7 0.8 - - - +
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Residues in contact with ASP 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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105A SER 2.8 19.7 + - - +
108A HIS* 1.3 91.5 + - + +
110A ARG* 1.3 67.8 + - - +
111A ASP* 3.2 21.2 + - - +
112A ILE* 3.5 32.1 - - + +
113A ALA* 3.4 13.3 + - - +
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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