Contacts of the strand formed by residues 111 - 121 (chain C) in PDB entry 2OKD
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 ARG 111 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25C GLN* 2.6 38.0 + - - +
33C ASP* 3.2 40.2 + - + +
34C LEU 3.5 11.0 - - - +
35C TYR* 3.8 15.7 - - + -
69C ARG* 3.4 32.0 - - + +
72C LEU* 3.9 14.0 - - - +
109C GLY 3.5 3.4 + - - -
110C ASP* 1.3 74.4 - - - +
112C ILE* 1.3 63.1 + - - +
113C ALA 4.2 5.6 - - - +
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Residues in contact with ILE 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C LEU 2.9 21.2 + - - +
35C TYR 4.1 4.7 - - - +
36C SER* 4.0 10.8 - - - +
50C ILE* 3.6 27.1 - - + +
52C THR* 4.7 4.3 - - + -
69C ARG* 5.1 3.6 + - - -
72C LEU* 3.9 16.0 - - + +
79C ILE* 4.1 3.5 - - - +
94C VAL* 3.7 31.4 - - + -
96C LEU* 3.5 34.5 - - + +
104C PHE* 6.1 0.9 - - + -
106C VAL* 4.1 25.1 - - + -
110C ASP* 3.6 12.6 - - + +
111C ARG* 1.3 79.0 - - - +
113C ALA* 1.3 64.9 + - - +
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Residues in contact with ALA 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ASP* 3.5 8.3 - - - +
34C LEU* 3.0 25.9 + - + +
66C ILE* 3.7 26.2 - - + -
67C ALA 3.5 12.6 - - - +
69C ARG* 4.3 12.7 - - - +
79C ILE* 4.0 7.0 - - + -
94C VAL* 4.1 11.2 - - + -
111C ARG* 3.9 3.3 - - - +
112C ILE* 1.3 83.5 - - + +
114C GLN* 1.3 61.4 + - - +
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Residues in contact with GLN 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A VAL* 3.4 31.4 + - - +
85A ASP* 4.1 10.1 + - - +
31C GLY 3.7 24.4 + - - -
32C TYR 3.6 6.1 - - - +
33C ASP* 3.7 15.9 - - - +
34C LEU* 5.2 0.2 - - - -
65C ARG 3.3 1.9 - - - +
66C ILE* 4.8 0.4 - - - -
67C ALA* 2.7 54.5 + - + +
68C PRO 3.1 21.7 + - - +
69C ARG* 3.7 28.6 + - - +
70C SER* 5.3 1.8 + - - +
113C ALA* 1.3 75.4 - - - +
115C LEU* 1.3 57.6 + - - +
116C ILE* 4.7 2.2 - - + -
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Residues in contact with LEU 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C PRO* 5.5 1.1 - - + -
31C GLY* 3.3 1.0 - - - -
32C TYR* 2.8 49.8 + - + +
34C LEU* 4.0 26.3 - - + +
56C MET* 3.7 21.8 - - + -
58C MET* 5.0 3.4 - - + -
64C GLY* 3.7 33.7 - - - +
65C ARG 3.3 6.3 - - - -
66C ILE* 4.0 18.8 - - + +
84C ILE* 4.4 7.4 - - + -
92C ILE* 4.9 4.7 - - + -
113C ALA 4.3 0.4 - - - -
114C GLN* 1.3 69.6 - - - +
116C ILE* 1.3 59.7 + - - +
117C TYR* 3.6 30.0 + - + +
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Residues in contact with ILE 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A TYR* 3.8 28.0 - - + +
83A VAL* 4.0 18.4 - - + -
120A ILE* 3.4 31.0 - - + -
30C ALA* 3.6 15.7 - - + +
31C GLY* 4.0 14.8 - - - -
63C TYR 3.3 0.5 - - - +
64C GLY* 3.4 2.5 - - - -
65C ARG 2.8 36.9 + - - +
67C ALA* 3.6 30.7 - - + -
114C GLN* 4.0 4.0 - - + +
115C LEU* 1.3 75.0 - - - +
117C TYR* 1.3 61.9 + - - +
118C GLN* 3.2 17.6 + - + +
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Residues in contact with TYR 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A ILE* 3.4 3.1 - - - +
121A TYR* 3.1 46.0 + - + +
123A PRO* 3.5 29.6 - - + -
125A LEU* 3.4 17.9 - - + +
10C VAL* 4.7 0.9 - - + -
30C ALA 5.0 1.0 + - - -
32C TYR* 3.4 36.7 - + - -
56C MET* 2.6 40.8 - - + +
58C MET* 3.8 17.3 - - + -
59C PRO* 3.7 25.6 - - + -
62C CYS* 4.6 4.9 - - - -
63C TYR 3.5 3.4 - - - -
64C GLY* 5.0 0.4 - - - -
115C LEU* 3.6 13.7 - - + +
116C ILE* 1.3 73.5 - - - +
118C GLN* 1.3 63.1 + - - +
119C ARG 3.6 0.5 + - - -
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Residues in contact with GLN 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A TYR* 2.6 24.6 + - - -
118A GLN* 2.9 13.7 - - - +
119A ARG 4.1 0.7 - - - -
120A ILE* 4.1 0.7 - - - -
200A CL 3.2 11.6 - - - +
204A EDO 2.8 40.3 + - - +
118B GLN* 3.6 0.4 - - - +
62C CYS* 3.3 2.6 - - - -
63C TYR* 2.9 48.3 + - + -
65C ARG* 3.2 30.5 + - + +
116C ILE* 3.6 21.2 - - + +
117C TYR* 1.3 72.5 - - - +
119C ARG* 1.3 63.7 + - - +
120C ILE* 3.6 3.7 + - - +
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Residues in contact with ARG 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A PHE* 5.6 4.8 - - - +
119A ARG* 3.1 43.7 + - + +
120A ILE 3.6 29.5 + - - -
121A TYR* 4.2 6.3 - - + -
204A EDO 3.6 4.9 + - - -
119B ARG* 3.0 63.0 + - + +
61C PHE 3.8 6.7 - - - +
62C CYS* 3.8 18.4 - - - -
118C GLN* 1.3 70.5 - - - +
120C ILE* 1.3 61.6 + - - +
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Residues in contact with ILE 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A EDO 4.1 1.6 - - - +
30B ALA* 3.7 22.2 - - - +
116B ILE* 3.4 23.8 - - + -
117B TYR 3.3 10.5 - - - +
118B GLN* 4.0 5.4 - - - -
119B ARG* 3.9 11.3 - - - +
61C PHE* 3.0 40.7 + - - +
62C CYS 3.8 18.2 - - - +
63C TYR* 3.6 22.2 - - + +
118C GLN 3.8 0.7 - - - +
119C ARG* 1.3 80.1 - - - +
121C TYR* 1.3 63.0 + - - +
122C TYR* 3.5 35.3 + - + +
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Residues in contact with TYR 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B ALA 5.1 1.4 - - - +
32B TYR* 4.5 1.4 - - - -
59B PRO* 5.2 7.9 - - + -
60B LYS 4.5 14.4 - - - -
61B PHE* 5.0 4.0 - - + -
62B CYS* 4.7 13.5 - - + -
117B TYR* 2.8 30.4 + - + +
119B ARG* 3.1 57.9 + - + -
61C PHE* 5.8 3.1 - + - -
120C ILE* 1.3 78.2 - - - +
122C TYR* 1.3 71.6 + - - +
123C PRO* 3.3 17.8 - - + +
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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