Contacts of the strand formed by residues 30 - 44 (chain A) in PDB entry 3BWB
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 30 (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* 3.1 25.3 - - - +
24A ASN* 5.6 0.4 - - - -
27A TRP* 3.1 51.5 + - + +
28A PRO 3.6 0.8 - - - +
29A GLY* 1.3 80.8 - - - +
31A ALA* 1.3 69.2 + - - +
246A PRO* 4.6 15.3 + - - -
247A CYS* 6.0 0.6 - - - +
19B TRP* 4.1 5.0 - - - -
32B MSE 3.6 28.3 - - + +
33B SER 3.6 6.5 - - - +
34B LEU* 3.6 13.6 - - + +
61B TRP* 3.3 31.4 - - - +
243B PRO 5.6 0.8 + - - -
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Residues in contact with ALA 31 (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 ARG* 3.8 39.9 - - + +
22A GLU 3.2 13.9 - - - +
23A GLU* 4.1 7.0 - - + -
24A ASN* 5.7 0.4 - - - +
30A GLN* 1.3 83.5 - - - +
32A MSE 1.3 61.3 + - - +
19B TRP* 4.2 4.0 - - + -
32B MSE 3.7 4.9 - - - +
33B SER* 2.8 34.3 + - - +
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Residues in contact with MSE 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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20A PHE* 5.2 0.3 - - - -
21A ARG* 3.5 2.1 - - - -
22A GLU* 2.7 50.8 + - + +
31A ALA* 1.3 75.4 - - - +
33A SER* 1.3 64.8 + - - +
34A LEU* 5.8 6.3 - - - -
61A TRP* 6.5 0.7 - - - -
71A ILE* 5.3 11.0 - - + -
243A PRO 4.1 10.8 - - - +
244A THR* 4.0 18.2 - - - +
245A TYR 3.9 13.5 - - - +
246A PRO* 3.8 27.1 - - + +
31B ALA 3.4 14.1 - - - +
32B MSE 4.0 17.7 - - + +
33B SER* 5.8 0.2 - - - -
246B PRO 4.9 10.3 - - - +
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Residues in contact with SER 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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19A TRP* 3.7 16.4 - - - -
20A PHE* 3.1 17.5 - - - -
21A ARG* 4.4 13.5 - - - -
32A MSE 1.3 77.9 - - - +
34A LEU* 1.3 66.7 + - - +
21B ARG* 4.7 3.5 + - - -
29B GLY 3.8 0.3 - - - +
31B ALA* 2.9 49.0 + - - +
33B SER* 5.0 4.7 + - - -
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Residues in contact with LEU 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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19A TRP* 3.4 4.6 - - - -
20A PHE* 2.7 41.8 + - + +
32A MSE 5.8 6.5 - - - -
33A SER* 1.3 82.0 - - - +
35A ARG* 1.3 62.7 + - - +
36A VAL* 3.5 0.7 + - - +
53A PHE* 4.3 13.7 - - + -
55A SER* 4.8 5.6 - - - -
61A TRP* 3.8 40.2 - - + -
64A VAL* 4.0 28.7 - - + -
71A ILE* 4.2 22.4 - - + -
74A THR* 5.4 1.1 - - + -
244A THR* 6.0 1.6 - - + -
29B GLY 3.4 12.1 - - - +
30B GLN* 4.0 8.7 - - + -
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Residues in contact with ARG 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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17A GLY* 4.4 11.7 + - - +
18A GLY 3.8 7.4 - - - +
19A TRP* 3.5 46.4 - - + +
34A LEU* 1.3 72.0 - - - +
36A VAL* 1.3 68.9 + - - +
53A PHE* 4.3 1.0 - - - -
55A SER* 3.6 6.9 - - - -
56A ASP* 2.9 53.5 + - + +
24B ASN* 4.4 11.5 - - - +
28B PRO* 4.9 6.5 - - - +
29B GLY* 2.9 26.4 + - - +
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Residues in contact with VAL 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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14A LEU* 3.2 31.4 - - + -
15A ILE 4.0 11.2 - - - +
17A GLY* 2.8 27.9 + - - -
18A GLY 2.7 17.1 + - - +
20A PHE* 3.6 11.9 - - + +
35A ARG* 1.3 76.6 - - - +
37A GLU* 1.3 60.6 + - - +
38A LYS 3.8 12.8 - - - +
39A VAL* 3.9 25.6 - - + -
53A PHE* 3.6 31.0 - - + -
54A GLU 3.9 2.9 - - - -
56A ASP* 5.2 0.4 - - - -
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Residues in contact with GLU 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 SER* 3.0 24.3 + - - -
17A GLY* 4.1 3.5 + - - -
35A ARG* 3.8 1.8 + - - +
36A VAL* 1.3 74.7 - - - +
38A LYS* 1.3 67.8 + - + +
54A GLU* 2.8 20.3 + - + +
55A SER 3.5 16.2 - - - +
56A ASP* 4.5 1.1 - - - +
57A PRO* 3.7 28.3 - - + +
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Residues in contact with LYS 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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16A SER* 3.8 7.4 - - - +
36A VAL* 4.0 2.9 - - - -
37A GLU* 1.3 86.6 - - + +
39A VAL* 1.3 73.5 + - - +
40A LEU* 3.6 20.7 + - + +
53A PHE* 3.4 1.0 - - - +
54A GLU* 2.7 43.8 + - + +
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Residues in contact with VAL 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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14A LEU* 3.8 39.5 - - + +
15A ILE* 4.1 5.2 - - - +
16A SER* 4.3 6.1 + - - +
36A VAL* 3.9 12.6 - - + -
38A LYS* 1.3 82.2 - - - +
40A LEU* 1.3 64.0 + - - +
41A TYR* 3.8 13.9 - - - +
42A ASP* 3.9 24.5 - - + +
51A THR* 6.0 0.7 - - + -
52A ILE 4.1 1.6 - - - +
53A PHE* 3.9 6.7 - - + -
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Residues in contact with LEU 40 (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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38A LYS* 3.6 39.0 + - + +
39A VAL* 1.3 74.4 - - - +
41A TYR* 1.3 68.5 + - - +
52A ILE* 3.0 16.6 + - + +
53A PHE* 4.2 1.1 - - - -
54A GLU* 4.2 14.4 - - + +
63A THR* 3.7 30.5 - - + -
138A HIS* 3.7 39.6 + - + +
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Residues in contact with TYR 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 VAL* 3.7 4.2 - - - +
40A LEU* 1.3 81.2 - - - +
42A ASP* 1.3 74.7 + - - +
43A ALA* 4.2 27.2 - - + +
44A PRO 5.0 4.2 + - - -
45A THR* 5.2 1.9 - - + +
50A LEU* 3.9 29.4 - - + -
51A THR* 3.4 1.9 - - - +
52A ILE* 2.7 50.0 + - + +
130A GLU* 4.5 15.8 + - + +
134A GLN* 3.2 45.3 + - + +
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Residues in contact with ASP 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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12A SER 3.1 29.7 + - - +
13A GLU* 3.7 10.4 + - - +
14A LEU* 3.8 18.1 + - + +
39A VAL* 3.9 16.3 - - + +
41A TYR* 1.3 79.1 - - - +
43A ALA* 1.3 64.2 + - - +
49A HIS* 3.0 24.3 + - - -
50A LEU 3.6 4.0 - - - -
51A THR* 3.0 14.9 + - + +
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Residues in contact with ALA 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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41A TYR* 4.2 17.1 - - + +
42A ASP* 1.3 77.4 - - - +
44A PRO* 1.3 79.8 - - + +
49A HIS* 3.5 14.3 + - - -
50A LEU* 3.0 31.3 + - - +
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Residues in contact with PRO 44 (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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41A TYR* 5.0 3.6 + - - -
43A ALA* 1.3 98.2 - - + +
45A THR* 1.3 67.6 + - - +
48A GLN 3.5 9.2 - - - +
49A HIS* 3.5 20.1 - - + +
130A GLU* 4.4 2.3 - - - +
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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