Contacts of the helix formed by residues 91 - 108 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87B PHE* 4.7 8.4 - - + -
162C VAL* 3.1 14.6 - - - +
163C ASN* 2.8 58.2 + - - +
32D ARG* 5.2 4.0 - - - +
89D SER 3.7 6.2 + - - +
90D LEU* 1.3 76.1 - - - +
92D HIS* 1.3 66.5 + - - +
93D CYS* 4.2 5.8 - - + +
94D VAL* 2.9 27.6 + - + +
95D LEU* 3.1 12.2 + - - +
131D THR* 5.5 2.5 + - + +
135D CYS* 3.7 23.1 - - - +
137D SER* 4.4 14.6 - - - +
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Residues in contact with HIS 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C ASN* 5.7 6.3 - - - -
27D PHE* 3.6 14.4 + - + +
28D ASN* 3.4 43.3 + - + +
30D CYS 3.0 27.4 + - - -
32D ARG* 3.4 37.6 + - + +
35D LEU* 3.8 24.6 - - + +
90D LEU 4.1 1.0 + - - -
91D GLU* 1.3 72.5 - - - +
93D CYS* 1.3 61.2 + - - +
95D LEU* 3.7 4.1 + - - +
96D MET 3.5 13.3 + - - -
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Residues in contact with CYS 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C ILE* 3.9 13.2 - - + -
161C PRO* 3.6 55.2 - - - -
162C VAL* 3.7 20.9 - - + -
27D PHE* 4.2 4.3 - - - -
28D ASN* 4.2 6.5 + - - -
91D GLU* 3.1 2.3 - - + +
92D HIS* 1.3 76.4 - - - +
94D VAL* 1.3 58.2 + - + +
96D MET* 3.3 3.6 + - - +
97D THR* 2.7 37.6 + - - +
134D LEU* 5.9 1.6 - - + -
217D LEU* 3.9 11.6 - - + +
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Residues in contact with VAL 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D LEU* 4.1 14.8 - - + -
91D GLU* 2.9 18.0 + - + +
93D CYS* 1.3 78.4 - - + +
95D LEU* 1.3 57.8 + - - +
97D THR* 3.7 6.7 - - - -
98D SER* 2.8 28.9 + - - -
127D THR* 3.6 21.8 - - - +
130D ALA* 3.9 9.5 - - + +
131D THR* 3.2 45.8 - - + +
134D LEU* 5.4 2.2 - - + -
135D CYS* 3.8 18.4 - - - -
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Residues in contact with LEU 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D ARG* 3.9 23.8 - - + +
35D LEU* 3.9 20.4 - - + -
36D VAL* 3.8 19.1 - - + -
39D ILE* 3.3 27.1 - - + +
81D PHE* 3.6 23.9 - - + -
85D THR* 3.6 26.2 - - + +
90D LEU* 4.0 17.3 - - + -
91D GLU 3.1 13.8 + - - +
92D HIS* 3.9 6.1 - - - +
93D CYS 3.3 0.2 - - - -
94D VAL* 1.3 78.9 - - + +
96D MET* 1.3 60.8 + - - +
98D SER* 3.4 13.4 + - - -
99D LEU* 3.5 4.3 + - - +
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Residues in contact with MET 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D PHE* 3.7 33.7 - - + -
35D LEU* 4.2 18.2 - - + -
39D ILE* 4.0 16.8 - - - -
92D HIS 3.5 4.6 + - - +
93D CYS 3.3 5.4 + - - +
95D LEU* 1.3 76.2 - - - +
97D THR* 1.3 66.6 + - - +
99D LEU* 3.2 25.4 + - + +
100D TYR* 3.2 12.6 + - - +
217D LEU* 3.6 21.7 - - + +
220D TYR* 3.6 21.6 - - + +
221D TYR* 3.4 35.7 - - - +
224D ILE* 4.2 8.1 - - + -
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Residues in contact with THR 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D CYS* 2.7 24.6 + - - +
94D VAL* 3.8 4.3 - - - -
96D MET* 1.3 76.5 - - - +
98D SER* 1.3 57.7 + - - +
100D TYR* 3.3 3.7 + - + +
101D TYR* 2.9 63.4 + - + +
130D ALA* 3.9 12.8 - - + -
134D LEU* 3.9 13.6 - - + +
172D PRO* 3.9 17.2 - - + +
217D LEU* 3.5 20.9 - - - +
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Residues in contact with SER 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D ILE* 5.8 0.7 - - - -
81D PHE* 4.6 3.8 - - - -
94D VAL 2.8 18.7 + - - -
95D LEU* 3.5 9.4 - - - -
96D MET 3.2 0.2 - - - -
97D THR* 1.3 77.4 - - - +
99D LEU* 1.3 60.4 + - - +
101D TYR* 3.4 15.5 + - - +
102D ILE* 3.7 0.5 + - - +
122D PHE* 3.7 17.5 - - - -
123D LEU* 4.3 17.8 - - - +
126D ALA* 3.6 14.1 + - - -
127D THR* 3.4 34.8 + - - -
130D ALA* 5.0 0.2 - - - +
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Residues in contact with LEU 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D ILE* 4.0 24.4 - - + +
42D MET* 3.6 28.0 - - + -
43D LEU* 3.8 23.1 - - + -
46D LEU* 5.9 3.1 - - + -
95D LEU 3.5 3.6 + - - +
96D MET* 3.2 23.1 + - + +
98D SER* 1.3 75.8 - - - +
100D TYR* 1.3 63.7 + - - +
102D ILE* 3.3 25.3 + - + +
103D ASP* 3.9 2.8 + - - +
220D TYR* 4.0 23.0 - - + -
224D ILE* 3.3 28.7 - - + -
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Residues in contact with TYR 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D MET 3.2 10.3 + - - +
97D THR* 3.8 7.4 - - + +
99D LEU* 1.3 73.4 - - - +
101D TYR* 1.3 86.0 + + - +
102D ILE 3.0 5.5 + - - -
103D ASP* 3.1 2.8 + - - +
104D LEU* 3.0 24.2 + - + +
172D PRO* 3.7 29.9 - - + +
173D ARG 4.2 2.0 + - - -
174D ASP 6.1 0.4 - - - -
176D ASN* 3.1 37.4 + - - +
177D ILE* 3.6 31.5 + - + +
216D VAL* 3.5 28.3 - - + -
217D LEU* 5.0 3.1 - - + -
220D TYR* 3.5 38.8 - + + -
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Residues in contact with TYR 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D THR* 2.9 34.7 + - + +
98D SER 3.5 8.5 - - - +
99D LEU 3.3 0.6 - - - -
100D TYR* 1.3 89.0 - + - +
102D ILE* 1.3 56.6 + - - +
104D LEU* 3.9 16.1 - - + +
105D LEU* 3.0 30.8 + - - +
122D PHE* 3.5 14.0 - - + -
126D ALA* 3.6 33.4 - - + -
129D VAL* 4.7 1.6 - - + -
130D ALA* 3.6 25.3 - - + -
134D LEU* 4.2 2.3 - - - +
162D PHE* 3.8 23.2 - + + -
170D ILE* 2.7 53.1 + - + +
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Residues in contact with ILE 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D LEU* 3.2 36.3 - - + -
46D LEU* 4.0 19.3 - - + -
98D SER 3.7 2.9 + - - +
99D LEU* 3.3 13.7 + - + +
100D TYR 3.0 0.6 - - - -
101D TYR* 1.3 74.1 - - - +
103D ASP* 1.3 77.6 + - - +
104D LEU 3.0 1.6 + - - -
105D LEU* 3.1 2.5 + - - +
106D GLN* 2.9 44.8 + - - +
112D PHE* 4.8 3.1 - - + -
114D LEU* 3.7 26.9 - - + -
122D PHE* 3.3 32.2 - - + -
123D LEU* 6.2 0.2 - - + -
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Residues in contact with ASP 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D LEU* 4.7 7.6 - - - +
99D LEU 3.9 1.3 + - - +
100D TYR 3.1 7.1 + - - +
102D ILE* 1.3 85.6 - - - +
104D LEU* 1.3 56.2 + - - +
106D GLN* 4.2 8.0 + - - +
107D THR* 2.6 31.7 + - - -
177D ILE* 3.8 9.4 - - + +
220D TYR* 2.7 42.4 + - + +
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Residues in contact with LEU 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D TYR* 3.0 25.6 + - + +
101D TYR* 3.9 26.5 - - + +
102D ILE 3.0 0.4 - - - -
103D ASP* 1.3 77.7 - - - +
105D LEU* 1.3 64.4 + - - +
106D GLN 3.2 1.2 + - - -
107D THR* 3.2 12.4 + - - -
108D VAL* 3.3 18.1 + - + +
162D PHE* 4.4 3.6 - - + -
166D VAL* 3.3 44.2 - - + -
169D ARG 3.9 7.2 - - - +
176D ASN* 4.3 4.7 - - - +
177D ILE* 3.7 30.5 - - + +
180D CYS* 4.0 21.3 - - + -
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Residues in contact with LEU 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D TYR* 4.2 11.9 - - + +
101D TYR 3.0 17.4 + - - +
102D ILE 4.0 1.6 - - - +
104D LEU* 1.3 79.8 - - - +
106D GLN* 1.3 60.7 + - - +
108D VAL* 4.4 4.5 - - + -
109D TYR* 3.2 46.3 + - + +
112D PHE* 3.6 29.7 - - + +
122D PHE* 3.6 29.2 - - + -
162D PHE* 4.0 16.8 - - + -
165D ARG* 3.9 18.2 - - + -
166D VAL* 4.3 11.4 - - + -
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Residues in contact with GLN 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D LEU* 5.0 7.0 - - - +
50D ASN* 3.4 15.3 + - - +
102D ILE* 2.9 37.2 + - + +
103D ASP* 4.2 9.8 + - - +
105D LEU* 1.3 78.8 - - - +
107D THR* 1.3 64.1 + - - +
109D TYR 3.8 10.4 + - - +
110D PRO* 4.5 3.6 - - - +
112D PHE* 4.0 25.2 - - + +
113D THR* 3.7 5.3 - - - +
114D LEU* 3.0 28.4 + - - +
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Residues in contact with THR 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D ASP 2.6 22.0 + - - -
104D LEU 3.2 6.7 + - - -
106D GLN* 1.3 81.2 - - - +
108D VAL* 1.3 60.0 + - - +
109D TYR 3.3 1.7 + - - -
110D PRO* 5.0 4.5 - - - +
177D ILE* 4.0 22.9 - - + +
181D SER* 3.7 20.5 + - - +
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Residues in contact with VAL 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D LEU* 3.3 20.6 + - + +
105D LEU* 4.4 5.4 - - - -
107D THR* 1.3 78.2 - - - +
109D TYR* 1.3 59.1 + - + +
110D PRO* 4.0 6.4 - - - +
165D ARG 3.6 19.7 - - - +
166D VAL* 4.5 5.2 - - + -
177D ILE* 4.3 3.6 - - + +
180D CYS* 3.5 33.4 - - + -
181D SER* 3.6 32.3 - - - +
184D GLN* 2.9 37.3 + - + +
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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