Contacts of the strand formed by residues 15 - 26 (chain B) in PDB entry 2OG9
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 ILE 15 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14B ARG* 1.3 71.7 + - - +
16B THR* 1.3 64.2 + - - +
17B TRP 4.0 2.0 - - - +
18B VAL* 3.8 21.1 - - + -
54B ILE* 3.8 26.2 - - + -
55B GLU 3.8 5.6 - - - +
56B THR* 4.2 3.1 - - + -
87B LEU* 3.3 37.9 - - + +
88B ILE* 3.6 2.7 - - - +
89B GLY* 2.7 28.8 + - - -
90B GLU 2.8 18.1 + - - +
92B PRO* 3.9 16.6 - - + -
98B LEU* 4.2 13.5 - - + -
126B LEU* 3.9 24.9 - - + -
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Residues in contact with THR 16 (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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14B ARG* 3.6 31.4 - - - +
15B ILE* 1.3 80.6 - - - +
17B TRP* 1.3 61.8 + - - +
55B GLU 3.0 10.3 + - - -
56B THR 3.5 11.8 + - - -
57B ALA* 3.7 20.9 - - + +
88B ILE* 4.6 10.6 - - - +
382B GLY* 3.2 8.2 - - - -
383B THR* 2.9 38.4 + - - -
385B PRO* 3.9 7.6 - - - +
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Residues in contact with TRP 17 (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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15B ILE* 3.8 2.3 - - - +
16B THR* 1.3 79.7 - - - +
18B VAL* 1.3 72.8 + - - +
19B ARG* 3.3 61.9 - - + -
53B GLU* 4.0 20.0 - - + -
54B ILE* 3.6 0.2 - - - -
55B GLU* 3.1 67.4 + - + +
88B ILE* 5.6 0.2 - - - -
380B GLN* 3.0 31.0 - - - +
381B VAL 3.4 15.9 - - - -
382B GLY 3.9 9.0 - - - -
383B THR 3.7 9.4 - - - +
384B ARG* 3.6 45.4 - - + +
385B PRO* 4.2 5.8 - - + -
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Residues in contact with VAL 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ILE* 3.8 19.7 - - + -
17B TRP* 1.3 83.8 - - - +
19B ARG* 1.3 68.9 + - - +
20B ILE* 4.6 1.1 - - + -
53B GLU 3.2 11.2 - - - +
54B ILE* 4.4 6.5 - - + -
84B ALA* 4.3 14.8 - - + +
87B LEU* 4.3 18.4 - - + -
88B ILE* 5.0 2.7 - - + -
122B PHE* 3.6 33.2 - - + -
380B GLN* 3.1 6.4 - - - +
381B VAL* 2.9 44.0 + - + +
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Residues in contact with ARG 19 (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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17B TRP* 3.3 31.7 - - + -
18B VAL* 1.3 75.6 - - - +
20B ILE* 1.3 69.2 + - - +
21B SER* 4.2 5.8 + - - +
51B PHE 3.7 0.5 - - - +
52B ALA* 3.4 2.9 - - - -
53B GLU* 2.8 78.1 + - + +
378B GLU* 4.5 16.5 + - - +
379B ALA 3.4 10.5 - - - +
380B GLN* 4.0 14.9 + - + -
384B ARG* 3.6 28.3 - - - +
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Residues in contact with ILE 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B VAL* 4.6 2.9 - - + -
19B ARG* 1.3 77.7 - - - +
21B SER* 1.3 64.8 + - - +
50B LEU* 4.2 6.5 - - + -
51B PHE 3.2 9.9 - - - +
52B ALA* 4.4 3.4 - - + -
77B PHE* 3.6 22.2 - - + +
80B ALA* 3.7 8.5 - - + +
81B ARG* 3.2 47.1 - - + +
84B ALA* 5.2 4.0 - - + -
121B ALA* 6.3 0.2 - - + -
122B PHE* 3.6 35.7 - - + -
378B GLU* 3.2 3.6 - - - +
379B ALA* 2.8 45.3 + - + +
380B GLN* 5.7 0.2 - - - -
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Residues in contact with SER 21 (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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19B ARG* 4.2 6.9 - - - +
20B ILE* 1.3 78.5 + - - +
22B SER* 1.3 61.3 + - - +
23B CYS* 3.7 0.7 - - - -
49B ILE 3.5 1.4 - - - +
50B LEU* 3.4 8.8 - - - +
51B PHE* 2.8 47.6 + - - +
53B GLU* 4.2 14.6 + - - -
77B PHE* 4.3 0.4 - - - -
367B LEU* 5.8 1.7 - - - +
371B VAL* 5.6 3.1 - - - -
375B THR* 4.1 20.0 - - - -
377B GLU 3.5 5.2 - - - -
378B GLU* 4.2 6.3 + - - +
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Residues in contact with SER 22 (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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21B SER* 1.3 70.5 - - - +
23B CYS* 1.3 60.2 + - - +
24B TYR* 3.5 25.4 + - - -
48B ALA* 5.1 2.6 - - - +
49B ILE 3.6 5.7 + - - -
50B LEU* 4.7 2.6 - - - +
73B GLY* 4.3 7.4 + - - -
77B PHE* 3.8 21.1 - - - +
375B THR* 3.5 2.6 - - - -
376B ARG* 2.9 26.3 + - - -
377B GLU* 2.8 34.8 + - - -
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Residues in contact with CYS 23 (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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21B SER* 3.7 1.3 + - - +
22B SER* 1.3 73.5 + - - +
24B TYR* 1.3 64.6 + - - +
25B LEU 3.5 1.6 + - - -
49B ILE* 2.7 45.7 + - - +
51B PHE* 3.9 18.4 - - + -
343B LEU* 3.7 29.6 - - - -
371B VAL* 3.9 22.7 - - + -
374B TRP* 3.6 26.2 - - - -
375B THR* 4.1 4.3 - - - +
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Residues in contact with TYR 24 (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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82A GLU* 5.5 3.8 - - - -
22B SER* 3.5 21.7 + - - -
23B CYS* 1.3 72.4 - - - +
25B LEU* 1.3 60.6 + - - +
26B PRO* 3.3 13.2 - - - +
46B GLU* 3.4 29.2 - - + +
47B ILE 3.7 1.8 - - - -
48B ALA* 3.7 26.9 - - + -
73B GLY 4.1 0.5 - - - -
74B PRO* 3.3 36.9 - - + +
374B TRP* 2.9 27.7 + - - +
376B ARG* 3.3 64.5 + - + +
377B GLU* 5.1 3.9 + - + -
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Residues in contact with LEU 25 (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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23B CYS 3.5 2.0 + - - -
24B TYR* 1.3 69.1 - - - +
26B PRO* 1.3 75.6 - - - +
27B LEU* 3.6 12.7 + - + +
46B GLU* 3.1 4.7 - - - -
47B ILE* 2.9 49.0 + - + +
49B ILE* 4.4 9.2 - - + -
339B TRP 3.3 28.9 - - - +
340B LEU* 3.4 27.8 - - + -
342B PRO* 4.5 7.4 - - + -
343B LEU* 4.2 17.0 - - + -
374B TRP* 3.6 30.5 - - + -
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Residues in contact with PRO 26 (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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24B TYR 3.3 11.0 - - - +
25B LEU* 1.3 94.0 - - - +
27B LEU* 1.3 64.2 + - - +
28B ALA 3.9 1.6 + - - -
45B THR 3.8 7.2 - - - +
46B GLU* 4.2 5.4 - - + +
374B TRP* 3.4 44.5 - - + +
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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