Contacts of the strand formed by residues 35 - 41 (chain B) in PDB entry 3S4S
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 GLU 35 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31B ILE* 3.4 4.2 - - - +
32B TYR* 2.9 36.3 + - + +
33B ASN* 5.9 0.2 - - + -
34B GLN* 1.3 76.9 - - - +
36B GLU* 1.3 74.6 + - - +
37B SER* 3.2 4.0 + - - -
51B THR* 3.4 34.2 + - + +
53B LEU* 3.6 23.7 - - - +
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Residues in contact with GLU 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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143A HIS* 4.1 10.4 + - + -
29B ARG* 2.8 45.1 + - + +
30B CYS 3.3 13.9 - - - +
31B ILE* 3.7 13.6 - - + +
34B GLN 3.9 2.2 + - - -
35B GLU* 1.3 73.3 - - - +
37B SER* 1.3 60.7 + - - +
38B VAL 4.4 0.9 - - - +
39B ARG* 2.8 43.1 + - - +
50B VAL* 3.6 32.5 - - + +
51B THR* 3.6 14.0 - - - +
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Residues in contact with SER 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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73A MET* 5.0 6.6 - - - +
9B TRP* 4.1 11.3 - - - -
30B CYS* 2.7 22.4 + - - +
32B TYR* 5.2 2.2 - - - -
35B GLU* 3.2 7.7 + - - -
36B GLU* 1.3 75.0 - - - +
38B VAL* 1.3 65.6 + - - +
50B VAL* 2.6 30.3 + - - -
51B THR* 3.3 19.0 + - - -
53B LEU* 4.3 10.1 - - - -
54B GLY* 3.6 20.0 - - - -
57B ASP* 5.5 0.3 + - - -
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Residues in contact with VAL 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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28B GLU 4.1 0.2 - - - +
29B ARG 3.8 0.2 - - - -
30B CYS* 3.0 43.1 + - + +
36B GLU* 4.4 0.9 - - - +
37B SER* 1.3 83.4 + - - +
39B ARG* 1.3 67.8 + - - +
47B TYR* 4.3 5.4 - - + -
48B ARG 3.5 13.9 - - - +
49B ALA* 4.5 0.2 - - - -
50B VAL* 3.8 4.0 - - - +
54B GLY* 3.9 11.7 - - - +
57B ASP* 4.4 7.2 - - + +
58B ALA* 3.9 27.8 - - + +
61B TRP* 3.6 35.0 - - + -
13C LEU* 5.3 1.8 - - + -
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Residues in contact with ARG 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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25B ARG* 4.5 3.2 - - - +
27B LEU* 3.9 16.7 - - - +
28B GLU 3.0 16.8 - - - +
29B ARG* 3.0 20.1 - - - +
36B GLU* 2.8 41.4 + - - +
38B VAL* 1.3 76.1 - - - +
40B PHE* 1.3 58.1 + - - +
41B ASP* 4.1 13.3 + - + +
46B GLU 4.2 0.3 - - - +
47B TYR* 3.5 7.8 - - - -
48B ARG* 3.0 43.3 + - + +
50B VAL* 4.0 10.3 - - + +
960B GOL 3.1 49.2 - - - -
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Residues in contact with PHE 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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26B LEU* 4.2 13.7 - - + -
27B LEU* 3.5 4.7 - - - +
28B GLU* 2.9 42.5 + - + +
39B ARG* 1.3 71.4 - - - +
41B ASP* 1.3 58.0 + - - +
42B SER* 3.7 25.8 - - - -
45B GLY 2.9 33.4 - - - -
46B GLU* 3.7 19.1 - - - -
47B TYR* 3.3 34.7 - + + -
68B LEU* 4.7 3.8 - - + -
71B ARG* 3.6 51.6 - - + -
72B ARG* 4.0 8.5 - - + -
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Residues in contact with ASP 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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25B ARG* 2.7 44.3 + - - +
26B LEU 3.7 4.9 - - - +
27B LEU* 4.1 9.8 - - + +
39B ARG* 4.1 13.4 + - - -
40B PHE* 1.3 74.9 - - - +
42B SER* 1.3 53.6 + - - +
43B ASP* 2.7 17.8 + - - +
44B VAL* 2.5 51.4 + - + +
45B GLY 3.1 7.8 + - - -
46B GLU 4.1 5.3 + - - -
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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