Contacts of the strand formed by residues 31 - 47 (chain B) in PDB entry 2O07
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 GLN 31 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A TRP* 3.7 7.3 - - - -
33A LEU* 4.5 10.1 - - + +
34A SER 3.4 7.2 - - - +
35A LEU* 4.1 15.9 - - + -
59A TYR* 2.7 30.6 + - + -
74A ARG* 4.8 0.7 + - - -
239A PRO* 5.6 0.2 - - - +
23B GLU 4.2 1.2 - - - +
24B THR* 4.5 3.5 - - - +
25B CYS 5.2 0.2 + - - -
28B TRP* 3.4 42.7 - - + +
29B PRO 3.2 3.1 - - - +
30B GLY* 1.3 79.9 + - - +
32B ALA* 1.3 64.6 + - - +
212B LEU* 3.4 15.5 - - - +
242B PRO* 4.2 4.6 - - - +
243B SER* 3.0 35.9 + - - +
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Residues in contact with ALA 32 (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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20A TRP* 4.0 7.4 - - + -
33A LEU* 3.4 10.9 - - - +
34A SER* 2.8 38.0 + - - +
22B ARG* 3.6 28.3 - - + -
23B GLU 3.3 19.7 - - - +
24B THR* 3.8 9.9 - - + -
28B TRP* 5.2 1.3 - - - -
31B GLN* 1.3 79.1 - - - +
33B LEU* 1.3 58.9 + - - +
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Residues in contact with LEU 33 (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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31A GLN* 4.6 10.5 - - + +
32A ALA 3.4 20.4 - - - +
33A LEU* 4.9 3.1 - - + +
21B PHE 3.9 0.7 - - - +
22B ARG* 3.7 0.2 - - - -
23B GLU* 2.9 43.7 + - - +
28B TRP* 5.8 0.4 - - - +
32B ALA* 1.3 73.2 - - - +
34B SER* 1.3 71.2 + - - +
35B LEU* 4.0 15.3 - - + -
69B ILE* 3.8 25.5 - - + +
239B PRO 4.5 7.4 - - - +
240B THR* 3.8 34.3 - - + +
241B TYR 5.9 1.3 - - - +
242B PRO* 6.3 3.1 - - + -
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Residues in contact with SER 34 (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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22A ARG* 4.6 11.5 + - - -
31A GLN* 3.3 5.9 - - - -
32A ALA* 2.8 41.7 + - - +
34A SER* 4.6 2.3 + - - -
20B TRP* 3.5 24.5 - - - +
21B PHE 3.1 10.8 - - - -
22B ARG* 3.2 31.5 - - - +
32B ALA 3.9 0.6 + - - -
33B LEU* 1.3 76.1 - - - +
35B LEU* 1.3 62.7 - - - +
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Residues in contact with LEU 35 (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 GLY 3.5 7.4 - - - +
31A GLN* 4.0 6.3 - - + -
20B TRP* 3.4 4.8 - - - -
21B PHE* 2.8 38.0 + - + +
33B LEU* 4.0 18.2 - - + -
34B SER* 1.3 80.8 - - - +
36B GLN* 1.3 64.1 + - - +
37B VAL* 3.6 2.8 + - - +
54B PHE* 4.3 15.0 - - + -
56B SER* 4.7 3.1 - - - -
59B TYR* 3.7 35.0 - - + -
62B VAL* 4.1 26.5 - - + -
69B ILE* 4.1 23.3 - - + -
72B THR* 4.2 13.0 - - + -
240B THR* 4.4 1.8 - - + -
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Residues in contact with GLN 36 (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 GLY* 3.0 37.5 + - - +
19B GLY* 3.5 12.9 - - - +
20B TRP* 3.3 34.3 - - + +
35B LEU* 1.3 71.8 - - - +
37B VAL* 1.3 64.2 + - - +
56B SER* 3.3 9.9 - - - -
57B LYS* 2.9 49.8 + - + +
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Residues in contact with VAL 37 (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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16B ILE* 3.8 29.8 - - + -
19B GLY* 2.7 25.9 + - - +
20B TRP 3.9 0.9 - - - -
21B PHE 3.7 25.1 - - - +
35B LEU 3.8 1.6 - - - +
36B GLN* 1.3 78.2 - - - +
38B GLU* 1.3 64.2 + - - +
39B GLN* 3.6 26.5 - - - +
40B LEU 4.0 3.4 - - - +
54B PHE* 3.9 22.2 - - + -
55B ARG 3.8 5.8 - - - +
56B SER* 4.3 1.3 - - - +
57B LYS* 4.5 1.1 - - - -
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Residues in contact with GLU 38 (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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36B GLN 4.0 1.8 + - - -
37B VAL* 1.3 75.8 - - - +
39B GLN* 1.3 58.7 + - - +
55B ARG* 2.7 61.1 + - + +
56B SER 4.4 3.1 - - - +
57B LYS* 4.0 19.6 - - + +
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Residues in contact with GLN 39 (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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37B VAL* 3.6 6.8 - - - +
38B GLU* 1.3 90.0 - - - +
40B LEU* 1.3 74.0 + - - +
41B LEU* 3.4 18.4 + - + +
54B PHE* 3.4 1.4 - - - +
55B ARG* 2.6 67.5 + - + +
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Residues in contact with LEU 40 (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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16B ILE* 4.1 18.6 - - + -
37B VAL* 4.0 4.8 - - - +
39B GLN* 1.3 88.7 + - - +
41B LEU* 1.3 58.8 + - - +
42B HIS* 4.1 9.2 - - - +
43B HIS* 4.5 13.0 - - + +
52B LEU* 3.4 33.4 - - + -
53B VAL 3.7 10.8 - - - +
54B PHE* 4.1 4.7 - - + -
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Residues in contact with LEU 41 (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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39B GLN* 3.4 27.8 + - - +
40B LEU* 1.3 75.7 - - - +
42B HIS* 1.4 63.6 + - - +
53B VAL* 3.0 22.1 + - + +
55B ARG* 3.7 33.9 - - + +
61B ASN* 3.3 34.8 - - - +
136B PHE* 3.7 41.1 - - + -
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Residues in contact with HIS 42 (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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40B LEU* 4.1 5.6 - - - +
41B LEU* 1.4 80.5 - - - +
43B HIS* 1.3 72.6 + - - +
44B ARG* 3.6 31.8 - - + +
51B ILE* 3.6 20.2 + - + +
53B VAL* 2.9 21.5 + - + -
132B VAL* 3.5 30.5 - - + +
136B PHE* 3.8 23.1 - + + -
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Residues in contact with HIS 43 (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 ALA* 4.4 21.7 - - + +
40B LEU* 4.5 12.6 - - + +
42B HIS* 1.3 82.2 - - - +
44B ARG* 1.3 57.7 + - - +
50B ASP* 2.4 44.2 + - - -
51B ILE 3.0 15.8 + - - -
52B LEU* 3.8 37.2 - - + +
53B VAL 3.9 0.6 - - - +
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Residues in contact with ARG 44 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42B HIS* 3.6 23.1 - - + +
43B HIS* 1.3 76.0 - - - +
45B ARG* 1.3 64.6 + - - +
46B SER 3.8 0.2 + - - -
50B ASP* 3.9 5.8 - - - -
51B ILE* 2.9 34.6 + - + +
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Residues in contact with ARG 45 (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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44B ARG* 1.3 76.4 - - - +
46B SER* 1.3 70.7 + - - +
47B ARG 4.2 5.1 + - - -
48B TYR 3.4 9.5 + - - -
49B GLN* 3.2 33.6 - - - +
50B ASP* 3.6 31.9 + - - +
51B ILE* 5.6 0.2 - - - -
66B ASP* 4.3 5.3 + - - -
128B ASP* 4.9 0.9 - - - +
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Residues in contact with SER 46 (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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44B ARG 3.8 2.6 + - - -
45B ARG* 1.3 91.8 + - - +
47B ARG* 1.3 63.8 + - - +
48B TYR 2.9 11.3 + - - -
49B GLN 2.9 17.1 + - - -
51B ILE* 4.0 5.4 - - - +
126B ASP* 2.5 38.9 + - - -
128B ASP* 3.5 25.8 - - - -
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Residues in contact with ARG 47 (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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45B ARG* 4.2 4.0 + - - -
46B SER* 1.3 73.8 - - - +
48B TYR* 1.3 102.4 + - + +
128B ASP* 5.0 0.6 + - - -
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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