Contacts of the helix formed by residues 119 - 136 (chain A) in PDB entry 2PKW
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 119 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MSE 3.6 22.1 - - - +
117A GLU* 2.7 24.5 + - - +
118A ARG* 1.3 75.1 - - + +
120A PRO* 1.3 61.1 - - - +
121A VAL* 3.0 22.7 + - - +
122A VAL* 3.1 23.2 + - + +
123A ALA* 2.9 24.6 + - - +
151A HIS* 4.2 0.9 - - - -
193A LEU* 4.7 1.2 + - - +
194A VAL* 3.8 24.7 - - + +
301A TRS 4.7 4.6 - - - +
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Residues in contact with PRO 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MSE 3.6 35.7 - - + +
23A TRP* 3.3 31.3 - - - +
24A GLY 5.4 0.2 - - - +
25A LEU* 3.9 5.2 - - + -
118A ARG 3.3 9.1 - - - +
119A ASN* 1.3 86.0 - - - +
121A VAL* 1.3 63.0 + - - +
123A ALA* 3.4 2.6 + - + +
124A ALA* 3.0 22.5 + - - +
151A HIS* 3.7 22.4 - - + +
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Residues in contact with VAL 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MSE 3.5 26.5 - - + -
3A ILE* 4.2 20.4 - - + -
25A LEU* 3.8 24.5 - - + -
35A LEU* 4.3 17.0 - - + -
44A LEU* 4.4 4.9 - - + -
119A ASN* 3.0 9.3 + - - +
120A PRO* 1.3 76.6 - - - +
122A VAL* 1.3 59.4 + - - +
124A ALA* 3.2 7.4 + - - +
125A LEU* 3.0 36.0 + - + +
193A LEU* 3.7 23.8 - - + -
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Residues in contact with VAL 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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98A GLY 3.2 26.5 - - - +
99A LEU* 5.8 0.9 - - + -
117A GLU* 3.3 21.1 - - + +
119A ASN* 3.1 28.8 + - + +
121A VAL* 1.3 73.1 - - - +
123A ALA* 1.3 60.6 + - - +
125A LEU* 3.2 10.3 + - + +
126A LEU* 2.8 28.3 + - + +
190A PHE* 3.8 22.4 - - + -
193A LEU* 4.0 7.2 - - + -
194A VAL* 3.6 22.4 - - + -
301A TRS 4.2 1.3 - - - -
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Residues in contact with ALA 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TRP* 3.3 28.7 - - + -
117A GLU* 3.7 13.8 - - + +
119A ASN 2.9 15.4 + - - +
120A PRO 3.7 3.1 - - - +
121A VAL 3.2 0.2 - - - -
122A VAL* 1.3 76.9 - - - +
124A ALA* 1.3 53.2 + - - +
126A LEU* 3.6 4.4 - - - -
127A ASP* 2.7 37.4 + - - +
149A LEU* 3.7 9.6 - - + +
151A HIS* 4.1 16.2 - - + -
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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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19A LEU* 4.6 7.7 - - + +
23A TRP* 3.7 35.2 - - + +
25A LEU* 5.0 0.9 - - + -
35A LEU* 4.6 4.7 - - + -
42A LEU* 3.6 20.0 - - + +
120A PRO 3.0 14.2 + - - +
121A VAL* 3.5 10.8 - - - +
123A ALA* 1.3 77.7 - - - +
125A LEU* 1.3 57.2 + - - +
127A ASP* 3.4 1.9 + - - +
128A ASP* 3.0 28.6 + - - +
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Residues in contact with LEU 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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35A LEU* 3.9 11.4 - - + -
42A LEU* 3.3 30.6 - - + +
43A GLU* 3.8 19.5 - - - -
44A LEU* 4.0 28.3 - - + +
55A ILE* 4.2 6.3 - - + +
56A PHE* 4.8 4.0 - - - -
57A VAL* 3.6 22.5 + - + +
99A LEU* 5.6 5.8 - - + -
121A VAL* 3.0 28.7 + - + +
122A VAL* 3.2 14.8 + - + +
124A ALA* 1.3 75.0 - - - +
126A LEU* 1.3 64.7 + - - +
128A ASP* 3.4 4.0 + - - +
129A GLY 3.1 16.3 + - - -
132A ARG* 4.7 0.5 + - - -
190A PHE* 5.4 6.1 - - + -
193A LEU* 4.7 1.6 - - + -
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Residues in contact with LEU 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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57A VAL* 3.9 14.1 - - + -
59A PHE* 4.6 1.3 - - + -
97A ALA* 3.5 25.6 - - + -
98A GLY 3.3 27.1 - - - +
99A LEU 3.6 22.9 - - - +
100A GLY* 3.8 8.1 - - - +
115A MSE 4.2 14.4 - - + -
117A GLU* 4.1 7.0 - - + -
122A VAL* 2.8 23.7 + - + +
123A ALA 3.8 3.1 - - - +
125A LEU* 1.3 69.8 - - - +
127A ASP* 1.3 68.0 + - - +
129A GLY* 3.0 2.4 + - - -
130A LEU* 2.9 29.9 + - - +
149A LEU* 3.9 22.4 - - + -
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Residues in contact with ASP 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 6.0 1.9 - - - +
22A ARG* 5.2 2.9 + - - -
23A TRP* 3.7 26.4 + - + -
123A ALA 2.7 22.9 + - - +
124A ALA* 3.6 4.9 - - - +
126A LEU* 1.3 74.2 - - - +
128A ASP* 1.3 57.3 + - - +
130A LEU* 3.2 11.3 + - - +
131A THR* 3.0 37.0 + - - -
149A LEU* 4.0 13.4 - - + +
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Residues in contact with ASP 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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40A GLN 4.9 1.2 - - - +
41A HIS* 3.3 4.2 - - - +
42A LEU* 2.9 41.3 + - + +
124A ALA 3.0 17.2 + - - +
125A LEU* 3.7 5.6 - - - +
127A ASP* 1.3 74.4 + - - +
129A GLY* 1.3 65.9 + - - +
131A THR* 3.5 9.4 + - - -
132A ARG* 2.7 55.3 + - - +
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Residues in contact with GLY 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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57A VAL* 3.5 22.4 - - - -
59A PHE* 3.6 16.6 + - - +
125A LEU 3.1 7.1 + - - -
126A LEU 3.0 7.6 + - - -
128A ASP* 1.3 80.1 - - - +
130A LEU* 1.3 56.0 + - - +
132A ARG* 3.4 18.9 + - - +
133A GLY* 2.9 22.5 + - - -
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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
----------------------------------------------------------
59A PHE* 3.2 26.5 - - + -
115A MSE 3.8 20.0 - - + -
126A LEU* 2.9 27.3 + - - +
127A ASP* 3.5 12.6 - - - +
129A GLY* 1.3 74.1 - - - +
131A THR* 1.3 57.1 + - - +
133A GLY* 3.0 1.2 + - - +
134A TYR* 2.6 74.5 + - + +
143A LEU* 5.2 1.1 - - + -
147A LEU* 4.3 8.1 - - + +
149A LEU* 3.7 36.8 - - + +
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Residues in contact with THR 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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127A ASP* 3.0 22.3 + - - -
128A ASP* 3.7 13.0 - - - -
129A GLY 3.4 0.2 - - - -
130A LEU* 1.3 79.4 - - - +
132A ARG* 1.3 67.2 + - + +
134A TYR* 3.2 9.8 + - - +
135A ALA* 3.1 21.5 + - + +
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Residues in contact with ARG 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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40A GLN* 3.6 21.3 - - - +
41A HIS* 3.4 15.9 - - - +
42A LEU 4.7 0.6 + - - -
56A PHE* 3.9 15.0 - - - +
57A VAL* 2.7 34.3 + - - +
58A ASP* 4.1 13.9 + - - +
59A PHE 5.3 0.2 - - - +
60A VAL* 4.0 12.3 - - + +
125A LEU 4.7 0.2 + - - -
128A ASP* 2.7 41.4 + - - +
129A GLY* 3.4 14.2 + - - +
131A THR* 1.3 82.4 - - + +
133A GLY* 1.3 63.3 + - - +
135A ALA* 3.4 15.2 + - - +
136A ASP* 3.4 8.3 + - - -
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Residues in contact with GLY 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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59A PHE* 4.9 3.1 - - - -
60A VAL* 4.1 15.0 - - - +
129A GLY 2.9 16.0 + - - -
130A LEU 3.0 3.3 + - - -
132A ARG* 1.3 78.0 - - - +
134A TYR* 1.3 60.8 + - - +
136A ASP* 3.1 15.9 + - - +
139A ILE* 3.9 3.8 - - - +
140A GLY* 3.2 12.8 + - - -
143A LEU* 3.7 20.0 - - - -
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Residues in contact with TYR 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 LEU* 2.6 50.3 + - + +
131A THR* 3.8 7.6 - - - +
133A GLY* 1.3 72.8 - - - +
135A ALA* 1.3 58.6 + - - +
136A ASP 3.8 0.7 - - - +
140A GLY* 3.1 23.4 - - - -
143A LEU* 3.6 20.2 - - + -
144A GLN* 3.3 65.0 + - + +
147A LEU 2.7 22.0 + - - -
148A GLN* 4.0 5.7 - - - +
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Residues in contact with ALA 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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131A THR* 3.1 16.7 + - + +
132A ARG* 3.7 8.1 - - - +
133A GLY 3.2 0.2 - - - -
134A TYR* 1.3 75.0 - - - +
136A ASP* 1.3 65.8 + - - +
137A ALA* 3.4 2.6 + - - +
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Residues in contact with ASP 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A VAL* 3.4 34.7 - - + +
132A ARG 3.4 4.8 + - - -
133A GLY 3.1 16.8 + - - +
134A TYR 3.8 0.9 - - - +
135A ALA* 1.3 78.4 - - - +
137A ALA* 1.3 63.9 + - - +
138A ASP* 3.0 14.6 + - - +
139A ILE* 2.7 36.7 + - + +
140A GLY* 3.0 25.0 + - - +
141A GLY 4.4 0.9 + - - -
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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
------------------------------------------------------------
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