Contacts of the helix formed by residues 118 - 135 (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 THR 118 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D THR* 4.3 2.2 - - - +
67D TYR* 3.2 12.4 - - - +
68D HIS* 3.5 34.5 - - + +
112D PHE* 3.6 22.1 - - + -
113D THR 2.9 25.3 + - - +
114D LEU* 3.3 6.1 - - - -
115D ASN* 2.9 28.3 + - - +
117D LEU* 1.3 83.1 - - - +
119D ALA* 1.3 64.2 + - - +
120D HIS 3.5 2.2 + - - -
122D PHE* 3.1 24.3 + - - +
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Residues in contact with ALA 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D LEU* 5.8 0.6 - - + +
47D ILE* 3.9 23.6 - - + -
77D ILE* 4.1 14.3 - - + +
114D LEU* 3.8 17.4 - - + +
115D ASN 2.9 14.5 + - - +
116D SER* 4.8 3.8 - - - -
117D LEU 3.7 1.0 - - - -
118D THR* 1.3 76.6 + - - +
120D HIS* 1.3 63.1 + - + +
122D PHE* 3.4 4.2 + - - +
123D LEU* 2.8 37.2 + - - +
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Residues in contact with HIS 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D SER* 5.5 1.3 - - - +
73D PRO* 3.4 38.5 - - + +
75D ILE* 2.8 34.0 + - + -
76D SER 4.2 4.6 + - - -
77D ILE* 4.3 17.8 + - + +
80D TYR* 3.8 35.9 - + + +
116D SER* 6.1 3.2 - - - -
117D LEU 5.6 0.6 + - - -
118D THR 3.6 0.6 - - - -
119D ALA* 1.3 86.6 - - + +
121D ARG* 1.3 58.9 + - + +
123D LEU* 2.8 24.0 + - - +
124D LEU* 2.9 13.9 + - - +
294D MES 3.3 21.1 - - - +
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Residues in contact with ARG 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D ARG 3.7 11.6 + - - -
67D TYR* 3.5 36.3 - - - +
68D HIS 3.9 12.8 + - - -
69D SER* 4.0 14.3 + - - +
117D LEU 5.8 0.2 + - - -
118D THR 3.8 1.4 + - - -
119D ALA 3.6 0.2 - - - -
120D HIS* 1.3 75.6 - - - +
122D PHE* 1.3 52.2 + - - +
124D LEU* 3.6 6.6 + - - +
125D THR* 2.6 37.2 + - - -
150D VAL* 4.6 8.8 - - + +
154D GLU* 3.7 35.4 + - - +
158D LEU* 4.1 21.8 - - + +
294D MES 3.6 35.7 + - - +
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Residues in contact with PHE 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D LEU* 6.3 0.4 - - + -
67D TYR* 3.8 17.6 - + + -
98D SER 3.7 10.5 - - - -
101D TYR* 3.5 32.1 - - + -
102D ILE* 3.3 30.1 - - + -
105D LEU* 3.6 27.1 - - + -
112D PHE* 3.6 25.8 - + + -
114D LEU* 4.8 2.9 - - + -
118D THR 3.1 21.7 + - - +
119D ALA* 3.5 4.7 - - - +
121D ARG* 1.3 76.0 - - - +
123D LEU* 1.3 64.7 + - + +
125D THR* 2.9 3.2 + - - -
126D ALA* 2.7 48.6 + - + -
162D PHE* 4.3 9.9 - + - -
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Residues in contact with LEU 123 (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* 5.7 0.7 - - + -
43D LEU* 4.3 17.7 - - + -
77D ILE* 4.3 21.1 - - + -
80D TYR* 4.6 10.8 - - + -
81D PHE* 3.6 60.6 - - + -
84D LEU* 4.3 4.7 - - + -
98D SER* 4.3 16.8 - - - +
102D ILE* 6.2 0.2 - - + -
119D ALA 2.8 13.1 + - - +
120D HIS* 2.8 10.4 + - - +
122D PHE* 1.3 87.1 - - + +
124D LEU* 1.3 58.7 + - - +
126D ALA* 4.0 0.6 - - - +
127D THR* 2.9 32.8 + - - -
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Residues in contact with LEU 124 (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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80D TYR* 3.5 18.3 - - + +
84D LEU* 4.1 12.2 - - + +
120D HIS 2.9 10.2 + - - +
121D ARG* 3.9 7.9 - - - +
123D LEU* 1.3 76.2 - - - +
125D THR* 1.3 56.3 + - - +
127D THR* 4.1 4.9 - - + -
128D THR* 2.7 45.6 - - + +
144D TYR* 3.7 25.4 - - + +
145D ALA* 5.1 0.2 - - - -
148D GLY* 3.8 13.7 - - - +
150D VAL* 3.7 41.3 - - + -
155D LEU* 3.8 15.4 - - + +
158D LEU* 5.0 6.1 - - + -
294D MES 5.4 0.2 - - - -
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Residues in contact with THR 125 (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* 4.0 7.0 - - + -
121D ARG 2.6 19.6 + - - -
122D PHE* 2.9 13.1 + - - -
124D LEU* 1.3 74.1 - - - +
126D ALA* 1.3 66.8 + - - +
127D THR 2.9 2.6 + - - -
128D THR* 3.1 11.6 + - - -
129D VAL* 3.3 18.3 - - + +
155D LEU* 4.5 6.0 - - + +
158D LEU* 3.1 38.5 - - - +
159D GLU* 4.2 7.0 - - - -
162D PHE* 3.6 33.7 - - + -
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Residues in contact with ALA 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D SER* 3.6 14.3 + - - +
101D TYR* 3.6 28.8 - - + -
122D PHE* 2.7 44.4 + - + +
123D LEU* 4.1 2.7 - - - +
125D THR* 1.3 73.0 - - - +
127D THR* 1.3 61.9 + - - +
129D VAL* 4.0 2.4 - - - -
130D ALA* 3.2 27.7 + - - +
162D PHE* 5.1 4.0 - - - -
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Residues in contact with THR 127 (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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81D PHE* 3.9 10.6 - - - -
84D LEU* 3.8 20.2 - - + -
88D SER* 6.3 0.2 - - - -
90D LEU* 3.3 31.8 - - + +
94D VAL* 3.6 9.2 - - - +
95D LEU* 5.4 0.2 - - - +
98D SER* 3.4 15.3 + - - -
123D LEU 2.9 19.3 + - - +
124D LEU* 3.6 3.6 - - + +
125D THR 2.9 0.4 + - - -
126D ALA* 1.3 80.5 - - - +
128D THR* 1.3 73.3 + - + +
129D VAL 3.3 1.1 + - - -
131D THR* 2.7 30.7 + - - -
144D TYR* 5.3 2.2 - - + -
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Residues in contact with THR 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D LEU* 2.7 31.9 - - + +
125D THR 3.1 6.8 + - - -
127D THR* 1.3 86.6 - - + +
129D VAL* 1.3 62.9 + - - +
131D THR* 4.6 2.0 - - - -
132D LYS* 3.0 33.4 - - - +
141D ASN* 5.4 0.2 + - - -
144D TYR* 3.6 47.9 - - + -
155D LEU* 3.8 18.1 - - + +
159D GLU* 4.2 4.5 + - - +
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Residues in contact with VAL 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C ILE* 4.6 5.3 - - + +
101D TYR* 4.7 1.1 - - + -
125D THR* 3.3 25.7 + - + +
126D ALA 4.1 2.9 - - - +
127D THR 3.3 0.4 - - - -
128D THR* 1.3 84.7 - - - +
130D ALA* 1.3 63.8 + - - +
131D THR 3.2 1.1 - - - -
132D LYS* 3.8 3.5 - - - +
133D GLY* 2.8 27.9 + - - -
159D GLU* 3.8 30.3 - - + +
162D PHE* 4.2 17.0 - - + -
163D LEU* 3.6 28.7 - - + -
170D ILE* 4.2 17.2 - - + +
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Residues in contact with ALA 130 (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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94D VAL* 3.9 19.8 - - + +
97D THR* 3.9 22.2 - - + -
101D TYR* 3.6 19.6 - - + -
126D ALA 3.2 18.2 + - - +
129D VAL* 1.3 78.0 - - - +
131D THR* 1.3 56.6 + - - +
134D LEU* 3.0 45.4 + - + +
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Residues in contact with THR 131 (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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88D SER 5.6 0.9 - - - +
89D SER 5.5 5.2 - - - +
90D LEU* 3.6 12.2 - - + +
91D GLU* 5.7 2.2 - - + +
94D VAL* 3.2 23.0 - - + +
127D THR 2.7 23.1 + - - -
128D THR* 4.6 1.1 - - - -
129D VAL 3.2 0.4 - - - -
130D ALA* 1.3 75.7 - - - +
132D LYS* 1.3 64.3 + - - +
133D GLY 3.1 1.0 + - - -
135D CYS* 3.2 35.6 + - - +
137D SER 3.7 19.7 - - - +
138D PHE* 4.3 3.3 - - + +
144D TYR* 3.2 27.4 - - - +
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Residues in contact with LYS 132 (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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46C THR 2.7 29.2 + - - -
48C SER* 2.9 40.8 + - - +
51C ILE* 3.9 12.1 - - + +
52C ARG* 4.1 5.3 + - - -
128D THR* 3.0 23.1 - - - +
129D VAL 3.6 4.2 + - - +
130D ALA 3.5 0.2 - - - -
131D THR* 1.3 79.0 - - - +
133D GLY* 1.3 58.5 + - - +
134D LEU 3.6 0.2 - - - -
138D PHE* 4.3 18.2 - - + -
139D SER 4.5 4.9 - - - +
141D ASN* 3.0 31.1 - - - +
144D TYR* 4.0 21.5 - - + -
159D GLU* 2.7 23.1 + - - +
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Residues in contact with GLY 133 (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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48C SER 5.1 1.1 - - - -
51C ILE* 4.1 9.9 - - - -
52C ARG* 3.6 24.2 + - - +
55C SER* 4.7 2.8 + - - -
129D VAL 2.8 18.4 + - - -
132D LYS* 1.3 78.9 - - - +
134D LEU* 1.3 67.5 + - - +
170D ILE* 3.7 22.7 - - - +
171D ILE* 5.3 0.7 - - - +
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Residues in contact with LEU 134 (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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52C ARG* 3.3 10.3 - - - +
156C ARG* 3.5 11.4 + - - +
157C ALA* 5.3 3.8 - - + +
160C ILE* 4.7 24.8 - - + +
162C VAL* 3.4 20.0 - - + +
93D CYS* 5.9 1.3 - - + -
94D VAL* 5.4 3.4 - - + +
97D THR* 3.9 28.3 - - + +
101D TYR* 4.2 3.6 - - - +
130D ALA* 3.0 33.0 + - + +
133D GLY* 1.3 85.3 - - - +
135D CYS* 1.3 62.9 + - - +
170D ILE* 4.3 4.5 - - + +
171D ILE* 3.8 37.0 - - + +
172D PRO* 4.2 7.2 - - + -
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Residues in contact with CYS 135 (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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52C ARG* 2.8 22.3 + - - +
156C ARG* 4.6 0.2 - - - -
162C VAL* 3.7 20.2 - - + -
91D GLU* 3.7 20.2 - - - +
94D VAL* 3.8 26.9 - - - -
130D ALA 4.1 1.1 - - - -
131D THR* 3.2 23.0 + - - +
134D LEU* 1.3 83.8 - - - +
136D ASP* 1.3 67.4 + - - +
137D SER 3.5 15.9 - - - +
138D PHE* 4.0 12.0 - - - -
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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