Contacts of the strand formed by residues 31 - 47 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A GLU 4.2 1.6 - - - +
24A THR* 4.6 4.0 - - - +
25A CYS 5.3 0.2 + - - -
28A TRP* 3.5 41.2 - - + +
29A PRO 4.4 2.8 - - - +
30A GLY* 1.3 79.1 + - - +
32A ALA* 1.3 65.6 + - - +
212A LEU* 3.5 13.3 - - - +
242A PRO* 4.2 5.1 - - - +
243A SER* 2.9 37.4 + - - +
20B TRP* 3.6 6.8 - - - -
33B LEU* 4.6 10.4 - - + +
34B SER 3.3 7.4 - - - +
35B LEU* 4.0 15.9 - - + -
59B TYR* 2.6 31.4 + - + -
74B ARG* 5.0 0.5 + - - -
239B PRO* 5.5 0.6 - - - +
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Residues in contact with ALA 32 (chain A).
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* 3.7 29.2 - - + -
23A GLU 3.3 18.8 - - - +
24A THR* 4.0 8.7 - - + -
28A TRP* 5.3 1.6 - - - -
31A GLN* 1.3 79.0 - - - +
33A LEU* 1.3 57.3 + - - +
34A SER 3.9 0.2 + - - -
20B TRP* 4.0 8.5 - - + -
32B ALA 3.6 0.7 - - - +
33B LEU* 3.4 11.9 - - - +
34B SER* 2.8 36.9 + - - +
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Residues in contact with LEU 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A PHE* 3.8 0.7 - - - +
22A ARG* 3.5 0.5 - - - -
23A GLU* 2.8 50.0 + - - +
28A TRP* 6.1 0.2 - - - -
32A ALA* 1.3 73.5 - - - +
34A SER* 1.3 69.3 + - - +
35A LEU* 4.1 11.8 + - + -
69A ILE* 3.7 26.2 - - + +
239A PRO 4.4 6.7 - - - +
240A THR* 3.8 37.0 - - + +
241A TYR 6.0 1.3 - - - +
242A PRO* 6.4 2.0 - - + -
31B GLN* 4.5 9.6 - - + +
32B ALA 3.4 21.3 - - - +
33B LEU* 4.9 2.2 - - + +
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Residues in contact with SER 34 (chain A).
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* 3.6 24.6 - - - +
21A PHE 3.0 10.1 - - - -
22A ARG* 3.3 30.4 - - - +
32A ALA 3.9 0.4 + - - -
33A LEU* 1.3 74.2 - - - +
35A LEU* 1.3 65.3 + - - +
22B ARG* 4.4 12.3 + - - -
31B GLN* 3.4 5.9 - - - -
32B ALA* 2.8 42.3 + - - +
34B SER* 4.6 2.3 + - - -
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Residues in contact with LEU 35 (chain A).
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* 3.5 3.1 - - - -
21A PHE* 2.8 40.0 + - + +
33A LEU* 4.1 16.6 - - + -
34A SER* 1.3 81.4 - - - +
36A GLN* 1.3 63.5 + - - +
37A VAL* 3.5 3.5 + - - +
54A PHE* 4.2 15.9 - - + -
56A SER* 4.6 3.1 - - - -
59A TYR* 3.9 26.2 - - + -
62A VAL* 4.2 17.5 - - + -
69A ILE* 4.2 19.7 - - + -
72A THR* 4.2 25.1 - - + -
240A THR* 4.3 4.9 - - + -
30B GLY 3.5 10.5 - - - +
31B GLN* 4.1 8.7 - - + -
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Residues in contact with GLN 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A GLY 3.5 16.3 + - - +
20A TRP* 3.4 33.9 - - + +
35A LEU* 1.3 70.0 - - - +
37A VAL* 1.3 62.9 + - - +
56A SER* 3.2 10.1 - - - -
57A LYS* 2.9 50.9 + - + +
30B GLY* 2.9 38.5 + - - +
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Residues in contact with VAL 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ILE* 3.9 27.8 - - + -
19A GLY* 2.8 25.9 + - - +
20A TRP 4.0 2.2 - - - -
21A PHE* 3.6 26.5 - - + +
35A LEU 3.7 3.1 - - - +
36A GLN* 1.3 76.4 - - - +
38A GLU* 1.3 64.9 + - - +
39A GLN* 3.6 26.7 - - - +
40A LEU 3.9 2.9 - - - +
54A PHE* 3.9 23.6 - - + -
55A ARG 3.9 7.0 - - - +
57A LYS* 4.5 2.4 - - - +
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Residues in contact with GLU 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A GLN 3.9 2.4 + - - -
37A VAL* 1.3 75.4 - - - +
39A GLN* 1.3 61.9 + - - +
55A ARG* 2.7 59.2 + - + +
56A SER 4.3 12.8 - - - +
57A LYS* 4.0 20.8 - - + +
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Residues in contact with GLN 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A VAL* 3.6 6.4 - - - +
38A GLU* 1.3 81.8 - - - +
40A LEU* 1.3 80.8 + - - +
41A LEU* 3.4 17.8 + - - +
54A PHE* 3.4 0.7 - - - -
55A ARG* 2.6 71.5 + - - +
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Residues in contact with LEU 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ILE* 4.2 16.8 - - + -
37A VAL* 3.9 4.6 - - + +
39A GLN* 1.3 89.5 + - - +
41A LEU* 1.3 66.1 + - - +
42A HIS 3.9 11.2 - - - +
43A HIS* 4.3 13.5 - - + -
52A LEU* 3.4 33.4 - - + -
53A VAL 3.8 4.7 - - - +
54A PHE* 4.1 5.4 - - + -
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Residues in contact with LEU 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A GLN* 3.4 26.7 + - - +
40A LEU* 1.3 74.0 - - - +
42A HIS* 1.3 64.5 + - - +
53A VAL* 2.9 18.4 + - + +
54A PHE 3.9 2.7 - - - -
55A ARG* 3.7 35.7 - - + +
61A ASN* 3.3 31.6 - - - +
136A PHE* 3.5 44.6 - - + -
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Residues in contact with HIS 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A LEU* 3.8 4.8 - - - +
41A LEU* 1.3 82.2 - - - +
43A HIS* 1.3 63.9 + - - +
44A ARG* 3.6 56.9 + - + +
51A ILE* 3.8 19.0 + - + +
52A LEU* 3.3 4.2 - - - +
53A VAL* 2.8 40.5 + - + +
132A VAL* 3.7 30.4 - - + +
136A PHE* 3.9 23.6 - + + -
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Residues in contact with HIS 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A LEU* 4.3 16.6 - - + +
42A HIS* 1.3 78.6 - - - +
44A ARG* 1.3 68.7 + - - +
50A ASP* 2.9 35.0 - - - -
51A ILE 3.3 10.3 + - - -
52A LEU* 3.9 25.9 - - + +
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Residues in contact with ARG 44 (chain A).
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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42A HIS* 3.6 36.0 + - + +
43A HIS* 1.3 79.6 + - - +
45A ARG* 1.3 61.0 + - - +
50A ASP* 4.0 6.3 - - - -
51A ILE* 2.8 40.2 + - + +
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Residues in contact with ARG 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ARG* 1.3 75.6 - - - +
46A SER* 1.3 67.2 + - - +
47A ARG 5.2 1.8 + - - -
48A TYR 3.9 6.5 + - - -
49A GLN* 3.5 30.6 - - - +
50A ASP* 3.5 35.9 - - - +
66A ASP* 4.3 5.3 + - - -
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Residues in contact with SER 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ARG 3.9 1.6 + - - -
45A ARG* 1.3 86.4 + - - +
47A ARG* 1.3 64.4 + - - +
48A TYR 3.0 9.2 + - - -
49A GLN 2.9 17.4 + - - -
51A ILE* 3.8 14.3 - - - +
126A ASP* 2.4 39.7 + - - -
128A ASP* 3.6 19.3 - - - -
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Residues in contact with ARG 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ARG* 5.2 2.1 + - - -
46A SER* 1.3 73.8 - - - +
48A TYR* 1.3 112.6 + - + +
128A ASP* 4.8 1.8 + - - -
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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