Contacts of the strand formed by residues 39 - 47 (chain B) in PDB entry 4PSQ
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 ASP 39 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B GLN* 1.3 80.3 - - - +
40B ASN* 1.3 88.0 + - - +
41B ILE* 3.2 6.6 + - - +
59B GLY* 3.5 1.9 - - - -
60B ARG* 2.5 69.9 + - - +
168B ILE* 3.4 21.3 - - + -
169B VAL* 3.8 21.1 - - - +
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Residues in contact with ASN 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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39B ASP* 1.3 102.7 + - - +
41B ILE* 1.3 60.0 + - - +
42B VAL* 3.4 7.2 + - - +
58B LYS* 3.2 13.0 - - - +
59B GLY* 3.6 3.5 - - - -
60B ARG* 4.5 6.2 - - + +
168B ILE* 3.8 1.0 - - - +
169B VAL* 3.0 30.5 + - - +
170B HIS* 3.8 11.9 + - - +
171B ASN* 2.8 29.5 + - - +
172B GLY 3.5 1.4 + - - -
173B TYR* 3.2 37.5 + - + +
174B CYS* 4.6 10.7 - - + +
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Residues in contact with ILE 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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24B TRP 4.2 0.2 - - - +
26B ALA* 3.1 41.0 + - + -
29B LYS* 4.5 1.3 - - + -
37B LEU* 3.8 51.6 - - + +
38B GLN 4.1 7.4 - - - +
39B ASP* 3.7 15.0 - - - +
40B ASN* 1.3 72.2 - - - +
42B VAL* 1.3 65.4 + - - +
43B ALA* 5.8 0.7 - - + -
57B ALA* 5.2 5.6 - - + -
58B LYS 3.3 8.7 - - - +
59B GLY* 4.6 0.2 - - - -
135B PHE* 3.9 28.0 - - + -
137B PHE* 5.2 5.1 - - + -
168B ILE* 4.1 16.7 - - + +
170B HIS* 3.3 10.3 + - - -
201B 2WL 6.1 0.2 - - - -
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Residues in contact with VAL 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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23B THR* 3.8 28.0 - - + -
24B TRP 3.6 4.3 - - - +
25B TYR* 3.9 15.9 - - + -
40B ASN 4.1 6.5 - - - +
41B ILE* 1.3 77.5 - - - +
43B ALA* 1.3 64.7 + - - +
44B GLU* 4.2 3.3 + - + +
56B THR 3.8 0.9 - - - +
57B ALA* 3.4 2.9 - - - -
58B LYS* 3.1 37.8 + - + +
170B HIS* 3.8 19.7 - - + +
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Residues in contact with ALA 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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22B GLY 3.7 0.9 - - - +
23B THR* 3.5 2.9 - - - -
24B TRP* 2.8 36.4 + - + +
41B ILE* 4.2 2.4 + - + -
42B VAL* 1.3 76.7 - - - +
44B GLU* 1.3 60.5 + - - +
45B PHE* 3.7 26.5 - - + -
55B ALA* 5.6 0.2 - - + -
56B THR 3.3 7.4 - - - +
57B ALA* 4.4 8.1 - - + +
137B PHE* 4.1 22.4 - - + -
201B 2WL 5.4 4.5 - - + -
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Residues in contact with GLU 44 (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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22B GLY* 3.4 24.5 - - - -
23B THR* 2.7 28.2 + - - +
42B VAL* 4.2 3.4 + - + +
43B ALA* 1.3 72.5 - - - +
45B PHE* 1.3 66.3 + - - +
46B SER* 4.5 4.4 + - - -
55B ALA* 3.4 2.8 - - - -
56B THR* 2.8 45.5 + - + +
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Residues in contact with PHE 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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20B PHE* 3.7 35.9 - + + +
21B SER* 3.7 18.0 - - - -
22B GLY* 3.1 27.2 + - - +
24B TRP* 3.9 17.7 - + - -
43B ALA* 3.7 24.5 - - + -
44B GLU* 1.3 82.0 - - - +
46B SER* 1.3 66.1 + - - +
53B MET* 3.9 20.9 - - + -
54B SER 3.5 4.9 - - - -
55B ALA* 3.9 14.8 - - + -
77B PHE* 3.7 24.2 - + - -
104B HIS* 3.9 23.8 - + - -
106B ILE* 5.3 0.2 - - + -
137B PHE* 5.0 10.3 - + - -
201B 2WL 5.1 4.3 - + - -
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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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21B SER* 4.0 8.2 - - - -
44B GLU* 4.5 4.6 + - - -
45B PHE* 1.3 78.7 - - - +
47B VAL* 1.3 65.9 + - - +
48B ASP 4.3 0.2 - - - -
53B MET* 3.5 4.5 - - - +
54B SER* 2.9 49.7 + - - +
55B ALA* 5.0 0.5 - - - -
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Residues in contact with VAL 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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17B LYS* 3.5 46.9 - - + +
18B ALA* 4.0 10.1 - - + +
21B SER* 4.5 4.9 - - - -
46B SER* 1.3 82.8 - - - +
48B ASP* 1.3 65.7 + - - +
51B GLY* 3.7 33.0 - - - +
52B GLN 3.8 6.1 - - - +
53B MET* 4.4 6.3 - - + -
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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