Contacts of the strand formed by residues 111 - 121 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B GLN* 3.3 32.5 + - - +
33B ASP* 3.2 26.6 + - + +
34B LEU 3.6 9.0 - - - +
35B TYR* 3.7 24.5 + - + -
69B ARG* 2.7 76.6 + - - +
72B LEU* 3.8 3.5 - - - +
109B GLY 3.7 2.2 + - - -
110B ASP* 1.3 72.7 - - - +
112B ILE* 1.3 62.7 + - - +
113B ALA 4.4 1.8 - - - +
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Residues in contact with ILE 112 (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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34B LEU 2.9 20.0 + - - +
35B TYR 4.0 6.3 - - - +
36B SER* 4.0 20.4 - - - +
50B ILE* 3.6 27.1 - - + -
52B THR* 4.4 3.4 - - + -
69B ARG* 4.1 8.0 + - - +
72B LEU* 3.7 13.3 - - + +
79B ILE* 4.3 2.8 - - - +
94B VAL* 3.7 28.0 - - + -
96B LEU* 3.6 33.0 - - + +
104B PHE* 6.3 0.4 - - + -
106B VAL* 4.1 15.0 - - + -
110B ASP* 3.6 15.3 - - + +
111B ARG* 1.3 74.9 - - - +
113B ALA* 1.3 70.2 + - + +
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Residues in contact with ALA 113 (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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33B ASP* 3.6 7.6 - - - +
34B LEU* 2.9 25.9 + - + +
66B ILE* 3.9 23.8 - - + -
67B ALA 3.5 13.5 - - - +
69B ARG* 4.1 16.4 - - - +
79B ILE* 4.2 4.0 - - + -
94B VAL* 4.1 12.3 - - + -
111B ARG* 3.8 1.2 - - - +
112B ILE* 1.3 86.4 - - + +
114B GLN* 1.3 64.7 + - - +
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Residues in contact with GLN 114 (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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25B GLN* 5.9 2.1 + - - -
29B ALA* 5.8 0.7 - - - +
30B ALA* 4.0 4.3 + - - +
31B GLY* 3.0 34.8 + - - +
32B TYR 3.3 11.4 - - - +
33B ASP* 4.7 7.6 - - - +
34B LEU* 4.6 2.2 - - - -
65B ARG 3.4 0.5 - - - +
66B ILE* 3.7 3.5 - - - -
67B ALA* 2.9 46.5 + - + +
68B PRO 3.2 20.9 + - - +
69B ARG* 4.7 6.2 - - + +
70B SER* 5.5 1.0 + - - +
113B ALA* 1.3 77.3 - - - +
115B LEU* 1.3 59.7 + - - +
116B ILE* 4.5 2.0 - - + -
83C VAL* 3.5 28.2 + - - +
85C ASP* 4.2 6.9 + - - +
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Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B PRO* 6.2 1.1 - - + -
31B GLY* 3.0 1.9 - - - -
32B TYR* 2.7 52.2 + - + +
34B LEU* 4.2 16.6 - - + -
56B MET* 3.7 31.2 - - + -
58B MET* 5.0 3.1 - - - -
64B GLY* 3.8 22.2 - - - -
65B ARG 3.4 11.7 - - - +
66B ILE* 3.7 23.8 - - + -
84B ILE* 4.2 7.9 - - + -
92B ILE* 4.7 8.3 - - + -
114B GLN* 1.3 72.8 - - - +
116B ILE* 1.3 61.7 + - - +
117B TYR* 3.8 20.8 + - + +
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Residues in contact with ILE 116 (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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30B ALA* 3.8 13.5 - - + +
31B GLY* 3.8 15.7 - - - +
64B GLY* 3.3 2.9 - - - -
65B ARG 2.8 34.3 + - - +
67B ALA* 3.5 31.2 - - + -
114B GLN* 4.5 2.5 - - + -
115B LEU* 1.3 74.2 - - - +
117B TYR* 1.3 60.3 + - - +
118B GLN* 3.2 15.9 + - + +
63C TYR* 3.8 31.6 - - + +
83C VAL* 4.0 19.3 - - + -
120C ILE* 3.4 31.6 - - + -
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Residues in contact with TYR 117 (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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10B VAL* 3.9 8.3 - - + +
30B ALA 5.0 1.0 + - - -
32B TYR* 3.6 35.3 - + - +
56B MET* 3.1 31.7 - - - +
58B MET* 3.7 23.6 - - - -
59B PRO* 3.6 27.1 - - + -
62B CYS* 3.8 13.2 - - - -
63B TYR 3.8 3.6 - - - -
64B GLY* 5.1 1.3 - - - -
115B LEU* 3.8 17.1 - - + +
116B ILE* 1.3 71.5 - - - +
118B GLN* 1.3 60.6 + - - +
119B ARG 3.7 0.3 + - - -
120C ILE* 3.3 6.2 - - - +
121C TYR* 2.8 50.6 + - + +
123C PRO* 3.6 23.8 - - + -
125C LEU* 3.5 11.2 - - + +
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Residues in contact with GLN 118 (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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118A GLN* 3.5 2.6 + - - -
200A CL 3.3 13.9 - - - +
204A EDO 3.0 24.6 + - - +
62B CYS* 3.5 3.5 - - - -
63B TYR* 2.8 68.4 + - + +
65B ARG* 3.4 19.8 + - + +
116B ILE* 3.3 26.8 - - + +
117B TYR* 1.3 71.4 - - - +
119B ARG* 1.3 64.3 + - - +
120B ILE* 3.4 5.4 + - - +
63C TYR* 2.7 31.7 + - - -
118C GLN* 3.8 0.4 - - - -
119C ARG 4.0 1.8 - - - -
120C ILE* 4.0 0.9 - - - -
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Residues in contact with ARG 119 (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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119A ARG* 3.1 53.6 + - + +
204A EDO 3.3 11.6 - - - -
61B PHE 3.7 8.5 + - - +
62B CYS* 4.7 1.1 - - - +
118B GLN* 1.3 69.4 - - - +
120B ILE* 1.3 58.3 + - - +
119C ARG* 3.0 60.4 + - - +
120C ILE* 3.9 11.7 - - - -
121C TYR* 3.1 56.6 + - + -
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Residues in contact with ILE 120 (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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30A ALA* 3.3 31.9 - - - +
116A ILE* 3.5 15.7 - - + -
117A TYR 3.3 11.4 - - - +
118A GLN* 4.3 5.4 - - + -
119A ARG* 3.6 16.0 - - - -
204A EDO 4.7 0.2 - - - -
61B PHE* 3.0 39.1 + - - +
62B CYS* 3.8 12.6 - - - +
63B TYR* 3.5 30.3 - - + -
118B GLN 3.7 1.6 - - - +
119B ARG* 1.3 80.2 - - - +
121B TYR* 1.3 63.2 + - - +
122B TYR* 3.5 25.8 - - + +
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Residues in contact with TYR 121 (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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9A PRO 5.3 5.9 - - - -
30A ALA 5.0 2.3 - - - +
31A GLY* 5.8 0.7 - - - -
32A TYR* 5.6 0.3 - - - -
59A PRO* 4.0 26.9 - - + -
62A CYS* 4.3 11.4 - - - -
117A TYR* 3.1 24.1 + - + +
119A ARG* 4.4 24.5 - - + +
61B PHE* 5.3 7.4 - + - -
120B ILE* 1.3 79.0 - - - +
122B TYR* 1.3 79.2 + - - +
123B PRO* 3.1 47.4 - - + +
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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