Contacts of the helix formed by residues 91 - 109 (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 GLU 91 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A VAL* 3.3 8.6 - - + +
163A ASN* 2.6 53.7 + - - +
32B ARG* 5.3 2.5 - - - +
89B SER 3.1 13.3 + - - +
90B LEU* 1.3 74.3 - - - +
92B HIS* 1.3 67.8 + - - +
93B CYS* 4.7 3.1 - - + +
94B VAL* 3.1 27.6 + - + +
95B LEU* 3.2 11.4 + - - +
131B THR* 5.6 2.6 + - + +
135B CYS* 3.4 31.0 - - - +
137B SER* 4.4 13.1 + - - +
87D PHE* 4.3 17.3 - - + -
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Residues in contact with HIS 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ASN* 5.6 6.1 - - - -
27B PHE* 3.5 14.0 + - + -
28B ASN* 3.6 40.0 + - + +
30B CYS 2.8 30.2 + - - -
31B SER* 4.8 0.2 - - - -
32B ARG* 3.6 29.2 - - + +
35B LEU* 3.8 14.1 - - + +
90B LEU 3.9 0.8 + - - -
91B GLU* 1.3 73.0 - - + +
93B CYS* 1.3 56.7 + - - +
95B LEU* 2.8 34.4 + - - +
96B MET* 3.1 13.2 + - - +
86D LYS* 4.6 17.1 + - - -
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Residues in contact with CYS 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A ILE* 4.1 5.8 - - + -
161A PRO* 3.2 54.7 - - - -
162A VAL* 3.8 19.5 - - + -
27B PHE* 3.8 18.4 - - - -
28B ASN* 3.6 9.0 - - - -
91B GLU* 3.5 1.4 - - + +
92B HIS* 1.3 78.4 - - - +
94B VAL* 1.3 52.1 + - - +
96B MET 3.8 0.6 - - - +
97B THR* 2.5 39.4 + - - -
134B LEU* 6.0 0.4 - - - -
217B LEU* 3.8 11.0 - - + +
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Residues in contact with VAL 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A VAL* 5.4 0.2 - - + -
90B LEU* 4.5 10.3 - - + -
91B GLU* 3.1 19.9 + - + +
92B HIS 3.1 0.8 - - - -
93B CYS* 1.3 74.2 - - + +
95B LEU* 1.3 61.3 + - + +
97B THR* 3.6 5.6 - - - -
98B SER* 2.8 29.0 + - - +
127B THR* 3.5 20.6 - - - +
130B ALA* 3.5 12.1 - - + +
131B THR* 3.4 32.1 - - + +
134B LEU* 5.7 2.5 - - + -
135B CYS* 3.4 32.1 - - - -
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Residues in contact with LEU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ARG* 3.7 37.2 - - + +
35B LEU* 4.1 17.9 - - + -
36B VAL* 4.1 8.3 - - + -
39B ILE* 3.2 30.6 - - + +
81B PHE* 4.6 11.0 - - + -
85B THR* 4.4 9.2 - - + +
90B LEU* 3.6 43.5 - - + +
91B GLU 3.2 11.3 + - - +
92B HIS* 2.8 14.7 + - - +
94B VAL* 1.3 73.5 - - - +
96B MET* 1.3 61.5 + - - +
98B SER* 3.5 17.0 + - - -
99B LEU 3.5 2.8 + - - -
127B THR* 5.6 0.7 - - - +
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Residues in contact with MET 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B PHE* 3.6 32.3 - - + -
35B LEU* 4.2 23.6 - - + -
39B ILE* 4.3 11.7 - - - -
92B HIS 3.1 9.3 + - - +
93B CYS 3.9 4.0 - - - +
95B LEU* 1.3 72.1 - - - +
97B THR* 1.3 68.0 + - - +
99B LEU* 3.1 28.6 + - + +
100B TYR* 3.1 13.0 + - - +
217B LEU* 3.7 23.5 - - + +
220B TYR* 3.5 20.5 - - + +
221B TYR* 3.4 34.8 - - - +
224B ILE* 4.6 5.2 - - + -
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Residues in contact with THR 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A ILE* 5.2 0.2 - - - +
93B CYS* 2.5 25.1 + - - +
94B VAL* 3.6 5.2 - - - -
96B MET* 1.3 76.6 - - - +
98B SER* 1.3 55.7 + - - +
100B TYR* 3.2 6.1 + - + +
101B TYR* 2.8 63.7 + - + +
130B ALA* 3.7 15.9 - - + -
134B LEU* 3.8 18.8 - - + +
172B PRO* 4.0 7.5 - - + +
217B LEU* 3.6 20.7 - - - +
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Residues in contact with SER 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ILE* 5.9 0.2 - - - -
81B PHE* 4.6 4.9 - - - -
94B VAL 2.8 23.2 + - - -
95B LEU* 3.5 10.2 - - - -
96B MET 3.1 0.2 - - - -
97B THR* 1.3 72.7 - - - +
99B LEU* 1.3 64.2 + - - +
101B TYR* 3.2 18.3 + - - +
102B ILE* 3.6 3.7 + - - -
122B PHE* 3.9 11.4 - - - -
123B LEU* 4.5 14.8 - - - -
126B ALA* 3.9 10.7 - - - -
127B THR* 3.1 38.3 + - - -
130B ALA* 4.8 0.6 - - - +
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Residues in contact with LEU 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ILE* 3.8 26.4 - - + +
42B MET* 3.9 18.8 - - + -
43B LEU* 3.7 27.4 - - + -
46B LEU* 6.0 2.5 - - + -
95B LEU 3.5 4.7 + - - +
96B MET* 3.1 23.5 + - + +
98B SER* 1.3 78.4 - - - +
100B TYR* 1.3 63.8 + - - +
102B ILE* 3.0 30.0 + - + +
103B ASP* 4.0 1.7 + - - +
220B TYR* 3.8 24.7 - - + -
224B ILE* 3.5 28.3 - - + -
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Residues in contact with TYR 100 (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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96B MET 3.1 8.5 + - - +
97B THR* 3.3 9.6 - - + +
99B LEU* 1.3 79.8 - - - +
101B TYR* 1.3 80.8 + + - +
103B ASP* 3.0 20.6 + - - +
104B LEU* 3.1 15.0 + - + -
172B PRO* 3.6 31.3 - - + +
173B ARG 4.3 1.7 + - - -
176B ASN* 2.9 35.0 + - - +
177B ILE* 3.5 35.8 - - + +
216B VAL* 3.7 19.3 - - + -
217B LEU* 4.8 4.7 - - + -
220B TYR* 3.5 37.8 - + + -
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Residues in contact with TYR 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B THR* 2.8 40.9 + - + +
98B SER* 3.2 11.4 + - - +
99B LEU 3.2 0.2 + - - -
100B TYR* 1.3 87.6 - + - +
102B ILE* 1.3 56.3 + - - +
104B LEU* 3.6 12.8 - - + +
105B LEU* 3.0 31.0 + - - +
122B PHE* 3.4 13.2 - - + -
126B ALA* 3.9 20.0 - - + -
129B VAL* 4.5 2.9 + - + -
130B ALA* 3.9 25.4 - - + -
134B LEU* 4.2 2.1 - - - +
162B PHE* 3.6 29.5 - + + -
170B ILE* 2.6 55.0 + - + +
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Residues in contact with ILE 102 (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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43B LEU* 3.3 37.9 - - + -
46B LEU* 4.0 23.3 - - + -
98B SER 4.4 2.9 - - - +
99B LEU* 3.0 19.3 + - + +
101B TYR* 1.3 77.0 - - - +
103B ASP* 1.3 62.2 + - - +
104B LEU 3.1 0.5 + - - -
105B LEU* 3.9 0.5 - - - +
106B GLN* 2.7 55.9 + - + +
112B PHE* 4.8 3.1 - - + -
114B LEU* 3.7 18.6 - - + -
122B PHE* 3.2 37.0 - - + -
123B LEU* 6.3 0.2 - - + -
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Residues in contact with ASP 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LEU* 5.3 4.2 - - - +
99B LEU 4.0 0.9 + - - +
100B TYR 3.0 6.2 + - - +
102B ILE* 1.3 86.9 - - - +
104B LEU* 1.3 60.0 + - - +
106B GLN* 4.0 8.1 - - - +
107B THR* 2.8 31.2 + - - +
177B ILE* 4.3 12.4 - - + +
220B TYR* 2.8 37.3 + - - +
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Residues in contact with LEU 104 (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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100B TYR* 3.1 22.9 + - + +
101B TYR* 3.6 27.4 - - + +
102B ILE 3.1 0.4 - - - -
103B ASP* 1.3 76.3 - - - +
105B LEU* 1.3 55.8 + - - +
107B THR* 2.8 25.7 + - - -
108B VAL* 3.2 18.9 + - + +
162B PHE* 4.6 0.9 - - + -
166B VAL* 3.5 30.5 - - + -
169B ARG 3.5 22.4 - - - +
176B ASN* 3.8 9.0 - - - +
177B ILE* 3.7 37.2 - - + +
180B CYS* 4.6 8.7 - - + -
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Residues in contact with LEU 105 (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* 3.9 22.0 - - + +
101B TYR 3.0 14.3 + - - +
104B LEU* 1.3 78.4 - - - +
106B GLN* 1.3 57.6 + - - +
108B VAL* 4.1 4.0 - - + -
109B TYR* 2.8 57.4 + - + +
112B PHE* 3.7 24.7 - - + -
122B PHE* 3.7 26.2 - - + -
162B PHE* 3.7 20.4 - - + -
165B ARG* 4.1 13.2 - - + -
166B VAL* 4.0 21.7 - - + +
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Residues in contact with GLN 106 (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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46B LEU* 5.1 3.5 - - - +
50B ASN* 3.3 22.1 + - - +
102B ILE* 2.7 38.1 + - + +
103B ASP* 4.2 8.3 - - - +
105B LEU* 1.3 71.4 - - - +
107B THR* 1.3 59.6 + - - +
109B TYR 4.4 6.0 - - - +
110B PRO* 5.4 2.6 - - - +
112B PHE* 3.7 30.2 - - + +
113B THR* 3.6 7.4 - - - +
114B LEU* 2.8 33.5 - - - +
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Residues in contact with THR 107 (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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103B ASP* 2.8 21.2 + - - +
104B LEU 2.8 5.9 + - - -
106B GLN* 1.3 80.1 - - - +
108B VAL* 1.3 61.7 + - + +
109B TYR 3.8 1.3 - - - -
110B PRO* 5.4 2.1 - - - +
177B ILE* 3.9 26.3 - - + +
181B SER* 4.0 18.8 + - - +
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Residues in contact with VAL 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B LEU* 3.3 23.1 - - + +
105B LEU* 4.1 5.4 - - + -
107B THR* 1.3 91.0 - - + +
109B TYR* 1.3 60.4 + - - +
110B PRO* 3.4 11.1 - - - +
165B ARG* 3.5 21.8 - - - +
166B VAL* 4.3 7.2 - - + -
177B ILE* 4.6 4.0 - - + +
180B CYS* 3.9 27.8 - - + -
181B SER* 4.0 22.0 - - - +
184B GLN* 2.6 34.0 + - - +
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Residues in contact with TYR 109 (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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64B LEU 4.7 1.6 + - - -
65B THR* 3.4 41.1 - - + +
66B ARG* 4.9 1.7 + - - +
67B TYR* 3.9 14.1 - + - -
105B LEU* 2.8 33.0 + - + +
106B GLN 4.4 3.5 - - - +
108B VAL* 1.3 79.0 - - - +
110B PRO* 1.3 74.1 - - + +
111B ASP* 3.2 22.1 + - + +
112B PHE* 3.0 32.3 + - + +
161B ASP* 4.4 1.4 + - - -
165B ARG* 3.1 61.8 + - + -
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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
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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