Contacts of the helix formed by residues 118 - 135 (chain B) in PDB entry 2PK9
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 118 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B THR* 4.3 1.1 - - - +
67B TYR* 3.1 19.1 - - + +
68B HIS* 3.7 28.3 - - + +
112B PHE* 3.8 19.3 - - + -
113B THR 2.8 16.7 + - - +
114B LEU* 3.3 3.3 - - - -
115B ASN* 2.6 50.8 + - - +
117B LEU* 1.3 74.1 - - - +
119B ALA* 1.3 66.2 + - - +
120B HIS 3.4 2.0 + - - -
121B ARG 3.7 1.0 + - - -
122B PHE* 3.0 21.9 + - - +
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Residues in contact with ALA 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 5.5 1.7 - - + +
47B ILE* 3.7 29.2 - - + -
77B ILE* 3.8 17.9 - - + -
114B LEU* 3.7 16.8 - - + -
115B ASN 3.2 6.7 + - - +
116B SER* 4.7 4.5 - - - -
117B LEU 3.9 1.2 - - - +
118B THR* 1.3 76.5 + - - +
120B HIS* 1.3 60.1 + - + +
122B PHE* 3.4 2.6 - - - +
123B LEU* 2.7 38.7 + - - +
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Residues in contact with HIS 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B SER* 5.4 1.1 - - - +
73B PRO* 3.0 42.6 + - + +
75B ILE* 2.8 34.3 + - + +
76B SER 4.1 0.7 - - - -
77B ILE* 3.7 35.7 - - + +
80B TYR* 4.0 25.4 - + + -
117B LEU 5.7 0.2 - - - -
118B THR 3.5 0.6 - - - -
119B ALA* 1.3 81.2 - - + +
121B ARG* 1.3 60.6 + - - +
123B LEU* 2.8 21.1 + - - +
124B LEU* 2.8 15.4 + - - +
294B MES 4.3 19.1 - - - -
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Residues in contact with ARG 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ARG* 2.8 28.5 + - - +
67B TYR* 3.6 23.1 - - - +
68B HIS 3.8 17.6 + - - -
69B SER* 3.5 25.3 + - - +
118B THR 3.7 2.2 + - - -
119B ALA 3.6 0.4 - - - -
120B HIS* 1.3 76.6 - - - +
122B PHE* 1.3 60.9 + - - +
124B LEU* 3.8 4.4 + - - +
125B THR* 2.9 29.6 + - - -
150B VAL* 5.2 3.4 - - + -
154B GLU* 2.7 35.1 + - - +
158B LEU* 3.7 27.6 - - + +
294B MES 4.0 22.0 + - - +
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Residues in contact with PHE 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 6.0 1.1 - - + -
67B TYR* 3.8 14.4 - + + -
98B SER 3.9 7.4 - - - -
101B TYR* 3.4 22.7 - - + -
102B ILE* 3.2 53.8 - - + -
105B LEU* 3.7 30.7 - - + -
112B PHE* 3.8 20.2 - + + -
114B LEU* 4.5 5.6 - - + -
118B THR 3.0 20.0 + - - +
119B ALA* 3.4 3.8 - - - +
121B ARG* 1.3 76.7 - - - +
123B LEU* 1.3 63.0 + - + +
125B THR* 3.2 3.1 + - - -
126B ALA* 2.7 43.2 + - + +
162B PHE* 3.9 12.1 - + - -
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Residues in contact with LEU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ILE* 5.9 0.7 - - + -
43B LEU* 4.4 15.7 - - + -
77B ILE* 3.7 25.4 - - + -
80B TYR* 4.0 18.4 - - + -
81B PHE* 3.6 50.5 - - + -
84B LEU* 4.6 4.9 - - + -
98B SER* 4.5 12.1 - - - -
102B ILE* 6.3 0.2 - - + -
119B ALA 2.7 17.5 + - - +
120B HIS 2.8 10.5 + - - +
122B PHE* 1.3 77.5 - - + +
124B LEU* 1.3 67.7 + - - +
126B ALA* 3.0 12.5 + - - -
127B THR* 3.1 20.1 + - - +
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Residues in contact with LEU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B TYR* 3.4 20.4 - - - +
84B LEU* 4.0 17.4 - - + +
120B HIS 2.8 13.3 + - - +
121B ARG* 3.9 4.9 - - - +
123B LEU* 1.3 74.0 - - - +
125B THR* 1.3 60.5 + - - +
127B THR* 3.6 0.9 - - - +
128B THR* 2.9 41.4 + - + +
144B TYR* 3.6 23.6 - - + +
148B GLY* 3.9 11.9 - - - -
150B VAL* 3.6 43.5 - - + -
155B LEU* 3.9 15.0 - - + -
158B LEU* 4.9 7.2 - - + -
294B MES 4.5 2.2 - - - -
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Residues in contact with THR 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B TYR* 4.1 9.4 - - + -
121B ARG 2.9 20.9 + - - -
122B PHE 3.4 4.0 - - - -
124B LEU* 1.3 78.0 - - - +
126B ALA* 1.3 65.8 + - - +
128B THR* 3.1 5.1 + - - -
129B VAL* 3.1 30.3 + - + +
155B LEU* 4.5 8.5 - - - +
158B LEU* 2.9 49.6 - - - +
159B GLU* 4.2 1.6 - - - -
162B PHE* 3.8 25.1 - - + -
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Residues in contact with ALA 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B SER* 3.9 10.5 - - - +
101B TYR* 3.9 23.8 - - + -
122B PHE* 2.7 47.7 + - + +
123B LEU* 3.0 4.6 + - - +
125B THR* 1.3 72.7 - - - +
127B THR* 1.3 56.8 - - - +
129B VAL* 2.7 27.3 + - - +
130B ALA* 2.8 13.7 + - - +
162B PHE* 5.3 2.0 - - + -
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Residues in contact with THR 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B PHE* 4.0 13.2 - - - -
84B LEU* 3.9 18.8 - - + +
88B SER* 6.0 0.2 - - - -
90B LEU* 3.7 34.1 - - + +
94B VAL* 3.5 9.1 - - - +
95B LEU* 5.6 0.3 - - - +
98B SER* 3.1 19.2 + - - -
123B LEU* 3.1 16.6 + - - +
124B LEU* 3.6 2.2 - - + +
126B ALA* 1.3 75.3 - - - +
128B THR* 1.3 75.5 + - + +
131B THR* 2.9 30.8 + - - -
144B TYR* 5.3 1.6 - - + -
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Residues in contact with THR 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU* 2.9 28.0 + - + +
125B THR* 3.1 6.8 + - - -
126B ALA 2.9 2.6 + - - -
127B THR* 1.3 84.3 - - + +
129B VAL* 1.3 64.0 + - - +
131B THR* 4.1 5.8 - - - -
132B LYS* 3.4 30.8 + - - +
141B ASN* 5.0 1.6 + - - -
144B TYR* 3.7 44.0 - - + -
155B LEU* 4.2 14.6 - - + +
159B GLU* 4.6 7.6 + - - +
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Residues in contact with VAL 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ILE* 4.7 7.4 - - + -
101B TYR* 4.5 6.3 - - + -
125B THR* 3.1 26.2 - - + +
126B ALA* 2.7 10.7 + - - +
128B THR* 1.3 74.2 - - - +
130B ALA* 1.3 60.0 + - - +
131B THR 3.2 0.2 - - - -
132B LYS* 3.8 2.8 - - - +
133B GLY* 2.8 27.9 + - - -
159B GLU* 3.8 30.5 - - + +
162B PHE* 4.3 17.3 - - + -
163B LEU* 3.8 28.9 - - + -
170B ILE* 4.3 13.4 - - + +
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Residues in contact with ALA 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B VAL* 3.5 28.5 - - + +
97B THR* 3.7 29.2 - - + -
98B SER* 4.8 0.9 - - - +
101B TYR* 3.9 14.2 - - + -
126B ALA 2.8 13.8 + - - +
127B THR 4.4 0.2 - - - -
129B VAL* 1.3 77.7 - - - +
131B THR* 1.3 60.3 + - - +
134B LEU* 3.0 33.5 + - + +
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Residues in contact with THR 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B SER 5.7 2.7 - - - +
89B SER 5.9 3.1 - - - +
90B LEU* 3.9 14.6 - - + +
91B GLU* 6.1 3.1 - - + +
94B VAL* 3.4 20.0 - - + +
127B THR 2.9 18.0 + - - -
128B THR* 4.5 2.2 - - - -
129B VAL 3.2 0.4 - - - -
130B ALA* 1.3 74.8 - - - +
132B LYS* 1.3 65.2 - - - +
135B CYS* 3.0 37.4 + - + +
137B SER 3.5 23.3 - - - +
138B PHE* 3.8 5.3 - - + +
144B TYR* 3.4 24.2 + - - +
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Residues in contact with LYS 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A GLU* 2.9 21.7 + - - -
46A THR 2.8 29.5 + - - +
48A SER* 3.1 47.5 + - - +
51A ILE* 3.9 10.7 - - + +
52A ARG* 3.9 5.7 + - - -
128B THR* 3.4 19.4 + - - +
129B VAL 4.2 0.7 - - - +
131B THR* 1.3 78.1 - - - +
133B GLY* 1.3 59.3 + - - +
135B CYS 5.0 0.4 - - - +
138B PHE* 4.4 10.5 - - + -
139B SER 4.4 14.8 - - - +
141B ASN* 3.1 20.8 - - - +
144B TYR* 4.4 10.8 - - + -
159B GLU* 2.6 28.0 + - - +
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Residues in contact with GLY 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ILE* 3.9 8.5 - - - -
52A ARG* 3.1 30.0 + - - +
55A SER* 5.2 1.6 + - - -
129B VAL 2.8 18.3 + - - -
130B ALA 3.9 0.2 - - - -
131B THR 3.0 0.2 - - - -
132B LYS* 1.3 79.4 - - - +
134B LEU* 1.3 65.8 + - - +
170B ILE* 3.6 21.0 - - - +
171B ILE* 5.8 0.2 - - - +
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Residues in contact with LEU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ARG* 3.2 9.2 - - - +
156A ARG* 3.6 15.4 + - - +
157A ALA* 5.1 4.6 - - + +
160A ILE* 4.5 23.4 - - + +
162A VAL* 3.6 16.3 - - + +
93B CYS 6.0 0.4 - - - -
94B VAL* 5.7 2.2 - - + -
97B THR* 3.8 35.7 - - + +
101B TYR* 4.2 6.5 - - - +
130B ALA* 3.0 18.6 + - + +
133B GLY* 1.3 83.5 - - - +
135B CYS* 1.3 63.1 + - - +
170B ILE* 4.2 5.6 - - + +
171B ILE* 3.8 39.7 - - + -
172B PRO* 4.0 12.3 - - + -
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Residues in contact with CYS 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ARG* 2.7 24.1 + - - +
156A ARG* 4.9 0.4 - - - -
162A VAL* 3.7 21.8 - - - -
91B GLU* 3.4 24.5 - - - +
94B VAL* 3.4 32.8 - - - -
130B ALA 4.4 0.7 - - - -
131B THR* 3.0 19.0 + - + +
134B LEU* 1.3 80.9 - - - +
136B ASP* 1.3 63.7 + - - +
137B SER 3.8 11.4 - - - +
138B PHE* 3.9 12.7 - - - -
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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
------------------------------------------------------------
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