Contacts of the helix formed by residues 103 - 118 (chain A) in PDB entry 2PWA
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 GLN 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A TYR* 4.7 1.4 + - - -
102A GLY* 1.3 78.0 + - - -
104A TYR* 1.3 67.4 + - - +
105A SER* 4.2 14.4 - - - +
106A THR* 3.0 23.6 + - - +
107A ILE* 3.0 12.3 + - - +
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Residues in contact with TYR 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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102A GLY 4.9 0.9 - - - -
103A GLN* 1.3 72.3 - - - +
105A SER* 1.3 63.3 + - - +
107A ILE* 3.2 11.4 + - + +
108A ILE* 2.8 28.8 + - - +
134A GLY* 4.5 2.2 - - - -
135A GLY* 2.8 28.8 + - - -
136A GLY 2.7 30.2 + - - -
137A TYR 5.1 0.4 - - - -
138A SER* 3.6 18.4 - - - -
141A VAL* 3.3 27.8 - - + -
170A SER* 3.5 7.3 + - - -
3003A NO3 3.3 21.5 - - - +
3007A NO3 3.5 24.2 - - - -
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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
----------------------------------------------------------
103A GLN* 4.2 9.4 - - - +
104A TYR* 1.3 75.6 - - - +
106A THR* 1.3 65.0 + - - +
108A ILE* 3.6 6.3 + - - +
109A ALA* 3.0 26.3 + - - +
3003A NO3 3.1 22.1 + - - -
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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* 3.4 37.7 - - + -
60A TYR* 4.0 8.9 + - + +
95A VAL* 3.6 26.0 - - - +
103A GLN* 3.0 17.9 + - - +
105A SER* 1.3 82.4 + - - +
107A ILE* 1.3 60.2 + - - +
109A ALA* 3.2 6.9 + - - +
110A GLY 2.9 24.1 + - - -
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Residues in contact with ILE 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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38A ILE* 5.1 1.6 - - + +
95A VAL* 3.8 28.0 - - + +
96A LEU* 4.1 8.1 - - + -
102A GLY 3.8 13.5 - - - +
103A GLN 3.0 8.1 + - - +
104A TYR* 3.7 17.3 - - + +
106A THR* 1.3 77.0 - - - +
108A ILE* 1.3 62.7 + - - +
110A GLY* 3.2 2.8 + - - -
111A MET* 3.1 43.0 + - + +
133A LEU* 3.9 25.6 - - + -
141A VAL* 5.1 7.2 - - + -
3007A NO3 3.5 36.6 - - - +
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Residues in contact with ILE 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 TYR 2.8 20.3 + - - +
105A SER* 3.7 5.2 - - - +
107A ILE* 1.3 73.0 - - - +
109A ALA* 1.3 67.0 + - - +
111A MET* 3.1 6.5 + - + +
112A ASP* 3.0 27.8 + - - +
140A SER* 3.8 22.4 - - - +
141A VAL* 3.9 16.2 - - + +
144A ALA* 3.8 18.8 - - + -
147A ARG* 3.7 24.9 - - - +
3003A NO3 3.6 30.5 - - - +
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Residues in contact with ALA 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* 3.1 27.5 + - + +
105A SER 3.0 18.6 + - - +
106A THR* 3.2 8.3 + - - +
108A ILE* 1.3 76.4 - - - +
110A GLY* 1.3 58.0 + - - +
112A ASP* 3.2 12.1 + - - +
113A PHE* 2.8 24.9 + - - +
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Residues in contact with GLY 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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38A ILE* 4.6 4.0 - - - -
59A TYR* 3.4 22.6 + - - -
93A VAL* 4.1 6.1 - - - +
95A VAL* 3.7 11.4 - - - -
106A THR 2.9 10.9 + - - -
107A ILE 3.7 3.8 - - - -
108A ILE 3.2 0.4 - - - -
109A ALA* 1.3 77.5 - - - +
111A MET* 1.3 60.7 + - - +
113A PHE* 3.3 3.9 + - - +
114A VAL* 3.1 28.0 + - - +
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Residues in contact with MET 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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38A ILE* 4.4 7.8 - - + +
107A ILE* 3.1 35.7 + - + +
108A ILE* 3.5 7.6 - - - +
110A GLY* 1.3 73.3 - - - +
112A ASP* 1.3 66.2 + - - +
114A VAL* 3.1 2.3 + - - +
115A ALA* 3.1 17.8 + - - +
131A LEU* 3.7 28.7 - - + -
141A VAL* 3.8 29.2 - - + +
144A ALA* 3.6 17.3 - - + +
145A ALA* 3.4 32.3 - - + -
148A LEU* 3.6 27.5 - - + +
171A PRO* 4.7 2.5 - - + -
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Residues in contact with ASP 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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108A ILE* 3.0 24.3 + - - +
109A ALA* 3.5 10.7 - - - +
111A MET* 1.3 77.6 - - - +
113A PHE* 1.3 63.6 + - - +
115A ALA* 3.3 9.0 + - - +
116A SER* 3.2 21.0 + - - -
144A ALA* 4.5 3.6 - - - +
147A ARG* 2.9 39.5 + - - +
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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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36A TYR* 4.6 1.6 - + - -
56A VAL* 3.7 28.0 - - + -
57A LYS* 3.6 51.1 - - + -
59A TYR* 3.4 18.6 - - - +
93A VAL* 4.2 10.8 - - + -
109A ALA 2.8 6.4 + - - +
110A GLY 3.4 8.3 - - - +
111A MET 3.2 0.2 - - - -
112A ASP* 1.3 76.1 - - - +
114A VAL* 1.3 62.6 + - + +
116A SER* 3.1 6.7 + - - -
117A ASP* 2.7 67.1 + - + +
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Residues in contact with VAL 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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36A TYR* 3.5 48.2 - - + -
38A ILE* 3.8 19.7 - - + -
93A VAL* 3.9 11.7 - - + -
110A GLY 3.1 15.0 + - - +
111A MET 3.1 6.5 + - - +
113A PHE* 1.3 79.2 - - + +
115A ALA* 1.3 65.8 + - - +
117A ASP* 4.4 3.4 - - - +
118A LYS* 3.1 24.3 + - - +
129A ALA* 4.7 3.4 - - + -
148A LEU* 3.8 18.6 - - + -
153A VAL* 4.6 8.3 - - + -
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Residues in contact with ALA 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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111A MET 3.1 12.1 + - - +
112A ASP* 3.6 11.9 - - - +
113A PHE 3.2 0.4 - - - -
114A VAL* 1.3 77.4 - - - +
116A SER* 1.4 59.2 + - - +
118A LYS* 2.8 27.8 + - - +
119A ASN* 3.7 4.0 - - - +
147A ARG* 5.0 2.7 - - + +
148A LEU* 3.5 13.2 - - + +
151A SER* 3.5 29.8 - - - +
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Residues in contact with SER 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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112A ASP 3.2 11.0 + - - -
113A PHE* 3.1 9.0 + - - -
114A VAL 3.1 0.2 - - - -
115A ALA* 1.4 74.0 - - - +
117A ASP* 1.3 66.6 + - - +
118A LYS 3.1 2.0 - - - -
119A ASN* 3.0 29.7 + - - +
120A ASN* 4.4 2.5 + - - +
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Residues in contact with ASP 117 (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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36A TYR* 2.7 28.4 + - - +
56A VAL* 4.3 1.0 - - - +
113A PHE* 2.7 54.7 + - + +
114A VAL* 4.1 2.0 - - - +
116A SER* 1.3 73.8 - - - +
118A LYS* 1.3 58.8 + - - +
120A ASN* 2.8 52.1 + - - +
121A ARG* 2.8 33.5 + - - +
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Residues in contact with LYS 118 (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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36A TYR* 3.3 23.3 + - + +
114A VAL 3.1 11.3 + - - +
115A ALA 2.8 27.8 + - - +
117A ASP* 1.3 76.5 - - - +
119A ASN* 1.3 79.6 + - - +
121A ARG* 3.4 22.3 + - - +
123A CYS* 5.4 0.9 - - - +
127A VAL* 4.3 12.5 - - + +
151A SER* 3.1 42.8 + - - -
153A VAL* 3.7 17.5 - - + -
3005A NO3 3.2 33.9 + - - +
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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