Contacts of the helix formed by residues 121 - 137 (chain A) in PDB entry 4WPN
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 ASN 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A SER 4.9 0.2 + - - -
117A ASN* 2.8 34.7 + - - +
120A LEU* 1.3 84.6 - - - +
122A ASP* 1.3 66.9 + - - +
123A LEU 3.4 0.7 - - - -
124A ALA* 3.4 1.6 + - - +
125A GLY* 2.9 23.2 + - - -
297A TYR* 3.0 30.9 + - - +
601A 3ST 4.0 20.5 - - - +
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Residues in contact with ASP 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A GLU* 4.3 9.9 - - + +
113A LYS* 3.1 44.5 + - + +
117A ASN* 3.0 16.0 + - - +
118A ALA* 3.4 11.2 - - + +
121A ASN* 1.3 77.0 - - - +
123A LEU* 1.3 65.1 + - + +
125A GLY 3.3 0.2 + - - -
126A CYS* 2.9 27.6 + - - -
171A PHE* 3.3 19.0 - - - +
173A LEU* 5.8 0.2 - - + -
174A VAL* 3.4 26.5 - - + +
297A TYR* 4.5 3.5 + - - -
601A 3ST 4.8 2.6 - - - -
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Residues in contact with LEU 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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96A ILE* 3.6 31.4 - - + +
100A ARG* 3.9 33.9 - - + +
103A LEU* 4.1 9.0 - - + -
104A ALA* 3.8 20.0 - - + +
107A GLU* 5.2 3.1 - - + -
118A ALA 3.0 26.2 + - - +
119A TYR 3.7 10.9 + - - +
121A ASN 3.4 0.4 - - - -
122A ASP* 1.3 77.7 - - + +
124A ALA* 1.3 66.4 + - - +
126A CYS* 3.4 4.7 + - + +
127A ILE* 3.0 32.5 + - + +
173A LEU* 3.6 29.4 - - + -
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Residues in contact with ALA 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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100A ARG* 3.8 18.1 - - - +
119A TYR 4.0 0.6 + - - -
120A LEU 3.3 23.6 - - - +
121A ASN* 3.4 2.6 + - - +
122A ASP 3.4 0.4 - - - -
123A LEU* 1.3 76.2 - - - +
125A GLY* 1.3 58.0 + - - +
127A ILE* 3.9 6.5 - - - +
128A LYS* 2.9 50.0 + - + +
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Residues in contact with GLY 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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121A ASN 2.9 17.4 + - - -
122A ASP 3.7 0.9 - - - -
124A ALA* 1.3 75.4 - - - +
126A CYS* 1.3 57.7 + - - +
128A LYS* 4.1 5.1 - - - +
129A THR* 2.8 38.1 + - - -
174A VAL* 5.0 1.3 - - - -
601A 3ST 3.8 30.3 - - - -
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Residues in contact with CYS 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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96A ILE* 4.9 6.7 - - + -
122A ASP 2.9 16.2 + - - +
123A LEU* 3.6 13.0 - - + +
125A GLY* 1.3 75.7 - - - +
127A ILE* 1.3 59.8 + - + +
130A LEU* 3.0 31.5 + - - +
173A LEU* 3.2 31.6 - - + -
174A VAL* 3.2 38.7 - - - +
177A ILE* 3.6 22.6 - - + +
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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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93A ALA* 4.1 10.5 - - + +
96A ILE* 4.0 21.3 - - + +
97A GLU* 3.8 35.0 - - + +
100A ARG* 4.4 18.4 - - - +
123A LEU* 3.0 24.0 + - + +
124A ALA* 3.9 5.6 - - - +
126A CYS* 1.3 80.4 - - - +
128A LYS* 1.3 60.7 + - + +
130A LEU* 3.5 5.2 + - - +
131A ARG* 3.0 66.9 + - - +
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Residues in contact with LYS 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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124A ALA* 2.9 34.3 + - + +
125A GLY* 4.1 5.2 - - - +
127A ILE* 1.3 80.0 - - + +
129A THR* 1.3 58.0 + - - +
131A ARG* 3.4 7.6 + - - +
132A TYR* 3.0 27.9 + - - +
462A ALA* 4.6 3.3 - - + +
463A GLN* 5.9 0.3 + - - -
601A 3ST 5.8 3.4 - - - +
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Residues in contact with THR 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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125A GLY 2.8 25.1 + - - -
128A LYS* 1.3 73.2 - - - +
130A LEU* 1.3 61.5 - - - +
132A TYR* 3.3 1.9 + - - +
133A CYS* 2.9 32.2 + - - -
177A ILE* 3.8 20.6 - - + +
178A TRP* 3.9 12.1 + - + -
462A ALA* 3.8 18.6 - - + +
478A LEU* 3.7 30.7 - - + -
601A 3ST 3.3 18.5 + - - -
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Residues in contact with LEU 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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89A LEU* 3.8 34.1 - - + +
92A LEU* 3.7 23.6 - - + -
93A ALA* 3.4 38.6 - - + +
96A ILE* 3.9 13.7 - - + -
126A CYS 3.0 14.4 + - - +
127A ILE 3.7 3.8 - - - +
129A THR* 1.3 77.9 - - - +
131A ARG* 1.3 58.1 + - - +
133A CYS* 3.3 4.0 + - + +
134A ALA* 2.9 30.1 + - - +
177A ILE* 3.8 18.3 - - + +
180A ILE* 5.4 2.2 - - + -
181A GLY* 4.4 15.5 - - - +
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Residues in contact with ARG 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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90A TYR* 3.4 34.2 + - + -
93A ALA* 3.8 14.2 - - + +
94A ASP* 2.8 33.5 + - - +
97A GLU* 2.9 33.3 + - - -
127A ILE* 3.0 43.5 + - - +
128A LYS* 3.8 7.6 - - - +
130A LEU* 1.3 75.9 - - - +
132A TYR* 1.3 63.0 + - - +
134A ALA* 3.4 1.1 + - - -
135A GLY* 3.3 15.1 + - - -
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Residues in contact with TYR 132 (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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128A LYS 3.0 15.3 + - - +
129A THR 3.4 9.0 - - - +
131A ARG* 1.3 76.4 - - - +
133A CYS* 1.3 68.7 + - - +
135A GLY* 3.1 12.1 + - - -
136A TRP* 3.0 47.7 + + - -
462A ALA* 3.2 35.4 - - + -
463A GLN* 3.8 39.9 + - + +
478A LEU* 5.0 1.8 - - + -
479A GLY* 3.4 20.2 - - - -
480A GLU 3.7 1.7 + - - -
483A PHE* 4.0 12.3 - + - -
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Residues in contact with CYS 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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89A LEU* 5.0 1.8 - - + -
129A THR* 2.9 32.0 + - - +
130A LEU* 3.7 4.7 - - + +
132A TYR* 1.3 77.7 - - - +
134A ALA* 1.3 61.9 + - - +
136A TRP* 3.1 7.3 + - - +
181A GLY* 3.7 24.5 - - - +
182A PRO* 3.6 31.0 - - - -
185A SER* 2.7 27.7 + - - -
478A LEU* 4.3 5.2 - - - -
483A PHE* 3.7 21.8 - - + -
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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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86A GLY* 3.3 36.9 - - - +
89A LEU* 3.6 21.0 - - + +
90A TYR* 3.5 26.6 - - + +
130A LEU 2.9 17.6 + - - +
131A ARG 3.5 4.9 - - - +
132A TYR 3.3 0.2 - - - -
133A CYS* 1.3 75.8 - - - +
135A GLY* 1.3 61.2 + - - +
137A ALA* 3.4 9.9 + - - +
138A ASP* 5.1 1.4 + - - +
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Residues in contact with GLY 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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90A TYR* 3.2 19.8 + - - -
131A ARG 3.3 2.5 + - - -
132A TYR 3.1 10.3 + - - -
134A ALA* 1.3 78.4 - - - +
136A TRP* 1.3 59.9 + - - +
137A ALA 3.3 0.4 + - - -
138A ASP* 3.8 0.7 - - - +
139A LYS* 2.7 40.8 + - - +
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Residues in contact with TRP 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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132A TYR* 3.0 42.4 + + - -
133A CYS 3.1 3.9 + - - +
135A GLY* 1.3 78.6 - - - +
137A ALA* 1.3 66.9 + - - +
138A ASP 3.3 0.4 - - - -
139A LYS* 2.9 50.0 + - + -
140A ILE* 3.3 21.7 + - + +
185A SER* 3.6 0.2 - - - -
479A GLY 4.1 1.8 + - - -
480A GLU* 3.7 45.1 - - + -
483A PHE* 3.4 50.4 - + + -
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Residues in contact with ALA 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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82A ALA* 3.4 25.1 - - - +
83A SER* 5.3 0.2 - - - -
85A ARG* 3.4 17.8 + - + -
86A GLY* 3.7 12.6 - - - +
134A ALA* 3.4 14.0 + - - +
135A GLY 3.3 2.8 - - - -
136A TRP* 1.3 76.7 - - - +
138A ASP* 1.3 58.4 + - - +
139A LYS 3.5 1.0 + - - -
140A ILE* 3.8 11.7 + - - +
185A SER* 3.1 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