Contacts of the helix formed by residues 117 - 137 (chain A) in PDB entry 3PWH
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 117 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A VAL* 3.3 10.6 - - - +
113A ASN 3.5 20.6 - - - +
114A GLY* 4.1 9.2 - - - +
115A LEU 2.9 16.4 + - - +
116A VAL* 1.3 73.7 - - - +
118A GLY* 1.3 64.6 + - - +
119A THR* 3.7 7.3 + - - -
120A ARG* 3.2 31.5 + - - +
121A ALA 3.1 18.9 + - - -
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Residues in contact with GLY 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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40A VAL* 3.4 22.5 - - - +
43A TYR* 4.1 20.9 - - - -
117A THR* 1.3 73.6 - - - +
119A THR* 1.3 59.8 + - - +
121A ALA* 3.6 3.9 - - - +
122A ALA* 3.5 18.4 + - - +
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Residues in contact with THR 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A THR* 3.1 8.8 + - - -
118A GLY* 1.3 74.9 - - - +
120A ARG* 1.3 67.1 + - + +
121A ALA 3.0 1.8 - - - -
122A ALA* 3.0 8.6 + - + +
123A GLY* 3.0 19.2 + - - -
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Residues in contact with ARG 120 (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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114A GLY 4.7 6.0 + - - -
115A LEU* 3.3 53.3 + - - +
116A VAL* 5.7 0.7 - - - -
117A THR* 3.2 19.0 + - - +
119A THR* 1.3 81.7 - - + +
121A ALA* 1.3 56.5 + - - +
123A GLY* 3.8 2.6 - - - +
124A ILE* 2.9 44.5 + - + +
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Residues in contact with ALA 121 (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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40A VAL* 3.6 19.5 - - + -
43A TYR* 4.1 16.2 - - + -
44A PHE* 3.7 22.4 - - + -
117A THR 3.1 17.3 + - - +
118A GLY* 3.6 7.6 - - - +
119A THR 3.0 0.2 - - - -
120A ARG* 1.3 78.0 - - - +
122A ALA* 1.3 61.8 + - - +
124A ILE* 3.8 1.6 - - - +
125A ILE* 3.0 32.1 + - - +
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Residues in contact with ALA 122 (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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43A TYR* 5.5 3.5 - - + +
118A GLY 3.5 9.0 + - - +
119A THR* 3.0 11.0 + - + +
121A ALA* 1.3 77.9 - - - +
123A GLY* 1.3 63.7 + - - +
125A ILE* 3.3 10.9 + - - +
126A ALA* 3.0 23.2 + - - +
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Residues in contact with GLY 123 (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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119A THR 3.0 13.6 + - - -
120A ARG* 3.8 4.0 - - - -
122A ALA* 1.3 75.8 - - - +
124A ILE* 1.3 61.6 + - - +
126A ALA* 3.2 8.6 + - - +
127A ILE* 3.1 29.6 + - - +
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Residues in contact with ILE 124 (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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44A PHE* 3.7 24.2 - - + -
97A ALA* 5.1 5.4 - - + -
120A ARG* 2.9 28.2 + - + +
121A ALA 3.8 2.7 - - - +
123A GLY* 1.3 73.3 - - - +
125A ILE* 1.3 54.6 + - - +
127A ILE* 3.1 11.6 + - + +
128A CYS* 2.7 55.0 + - - -
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Residues in contact with ILE 125 (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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43A TYR* 3.1 40.8 - - + +
44A PHE* 3.6 22.7 - - + +
47A SER* 3.7 16.6 - - - +
121A ALA 3.0 27.1 + - - +
122A ALA* 3.6 8.5 - - - +
124A ILE* 1.3 75.9 - - - +
126A ALA* 1.3 63.9 + - - +
128A CYS* 3.2 9.5 + - - +
129A TRP* 3.0 47.1 + - + +
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Residues in contact with ALA 126 (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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122A ALA 3.0 14.0 + - - +
123A GLY* 3.4 11.0 - - - +
124A ILE 3.2 0.2 - - - -
125A ILE* 1.3 78.1 - - - +
127A ILE* 1.3 64.6 + - + +
129A TRP* 3.2 9.0 + - - +
130A VAL* 3.0 28.1 + - + +
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Residues in contact with ILE 127 (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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123A GLY 3.1 15.2 + - - +
124A ILE* 3.1 11.7 + - + +
126A ALA* 1.3 76.5 - - + +
128A CYS* 1.3 57.9 + - - +
130A VAL* 3.2 8.1 + - + +
131A LEU* 2.8 55.3 + - + +
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Residues in contact with CYS 128 (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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44A PHE* 5.5 2.5 - - - -
47A SER* 5.7 1.1 - - - +
90A SER* 5.1 4.5 - - - +
93A PHE* 3.3 52.8 - - + -
94A SER* 5.0 3.1 - - - +
124A ILE* 2.7 44.7 + - - -
125A ILE* 3.3 12.6 - - - +
126A ALA 3.2 0.2 - - - -
127A ILE* 1.3 74.8 - - - +
129A TRP* 1.3 59.1 + - + +
131A LEU* 3.6 1.7 + - - -
132A SER* 2.8 29.3 + - - -
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Residues in contact with TRP 129 (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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47A SER* 3.0 38.6 + - - +
50A ALA* 4.8 5.4 - - + -
51A ALA* 3.7 27.4 - - + -
54A LEU* 4.5 12.6 - - + -
86A VAL* 4.8 2.5 - - + -
87A LEU* 4.0 20.4 - - + -
90A SER* 3.2 26.0 + - - -
125A ILE* 3.0 38.8 + - + +
126A ALA* 3.2 7.6 + - - +
128A CYS* 1.3 73.9 - - + +
130A VAL* 1.3 66.1 + - + +
132A SER* 3.0 14.6 + - - -
133A PHE* 3.0 50.3 + + + -
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Residues in contact with VAL 130 (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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126A ALA* 3.0 23.0 + - + +
127A ILE* 3.6 11.0 - - + +
129A TRP* 1.3 78.2 - - + +
131A LEU* 1.3 69.6 + - + +
133A PHE* 3.3 7.6 + - - +
134A ALA* 3.2 20.7 + - + +
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Residues in contact with LEU 131 (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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93A PHE* 4.0 23.3 - - + -
127A ILE* 2.8 42.6 + - + +
128A CYS* 4.0 4.3 - - - +
130A VAL* 1.3 81.0 - - + +
132A SER* 1.3 57.6 + - - +
134A ALA* 3.7 9.8 - - + +
135A ILE* 3.1 38.1 + - + +
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Residues in contact with SER 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A VAL* 2.7 40.6 + - - +
89A GLN* 3.8 4.7 - - - +
90A SER* 3.1 20.4 + - - -
93A PHE* 3.9 7.2 - - - -
128A CYS 2.8 19.6 + - - -
129A TRP* 3.0 15.2 + - - -
131A LEU* 1.3 78.8 - - - +
133A PHE* 1.3 54.3 + - - +
136A GLY* 2.9 27.5 + - - -
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Residues in contact with PHE 133 (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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79A PHE* 5.6 3.8 - + - -
83A PHE* 4.8 16.8 - + - -
86A VAL* 4.0 23.3 - - + -
87A LEU* 6.2 0.4 - - + -
129A TRP* 3.0 55.4 + + + -
130A VAL* 3.8 7.6 - - - +
132A SER* 1.3 73.9 - - - +
134A ALA* 1.3 65.9 + - - +
135A ILE 3.2 0.4 - - - -
137A LEU* 3.0 52.0 + - + +
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Residues in contact with ALA 134 (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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130A VAL* 3.2 17.5 + - + +
131A LEU* 3.7 15.7 - - + +
132A SER 3.4 0.2 - - - -
133A PHE* 1.3 79.0 - - - +
135A ILE* 1.3 59.4 + - + +
137A LEU 4.2 0.2 - - - -
138A THR* 2.9 20.6 + - - -
141A LEU* 3.9 15.1 - - + +
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Residues in contact with ILE 135 (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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89A GLN* 3.4 33.9 - - + +
93A PHE* 4.3 8.3 - - + -
131A LEU* 3.1 20.1 + - + +
134A ALA* 1.3 79.6 - - + +
136A GLY* 1.3 59.9 + - - +
137A LEU 3.1 2.2 - - - -
138A THR* 2.7 14.7 + - - -
176A TYR* 2.7 28.2 + - - +
180A PHE* 3.5 17.0 - - + -
181A ASN* 5.6 4.9 - - - +
185A CYS* 3.5 33.7 - - + -
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Residues in contact with GLY 136 (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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82A CYS* 3.2 26.2 - - - +
85A LEU* 3.6 28.2 - - - +
86A VAL* 3.9 8.3 - - - -
89A GLN* 4.9 0.6 - - - +
132A SER 2.9 22.9 + - - -
135A ILE* 1.3 74.9 - - - +
137A LEU* 1.3 62.0 + - - +
138A THR 3.4 1.2 + - - -
139A PRO* 4.0 0.7 - - - +
176A TYR* 4.0 2.3 + - - -
181A ASN* 5.7 1.1 - - - -
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Residues in contact with LEU 137 (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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79A PHE* 4.7 15.9 - - + -
82A CYS* 3.6 34.8 - - + +
83A PHE* 4.2 4.9 - - + +
86A VAL* 3.7 10.8 - - + -
133A PHE* 3.0 46.8 + - + +
134A ALA 4.2 1.6 - - - -
136A GLY* 1.3 75.0 - - - +
138A THR* 1.3 58.2 + - - +
139A PRO* 3.3 4.7 - - - -
140A MET* 3.0 51.0 + - + +
141A LEU* 3.5 9.8 + - + +
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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
------------------------------------------------------------
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