Contacts of the strand formed by residues 35 - 41 (chain E) in PDB entry 5MS0
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 35 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29E ALA* 5.0 4.5 - - - +
34E ALA* 1.3 78.1 - - - +
36E VAL* 1.3 63.1 + - - +
76E ILE* 3.9 23.7 - - - +
77E VAL* 4.2 15.9 + - + +
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Residues in contact with VAL 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E VAL* 5.5 11.4 - - + +
29E ALA* 5.2 13.0 - - + -
30E LYS* 5.9 3.1 - - + +
34E ALA 4.3 0.4 + - - -
35E GLN* 1.3 76.5 - - - +
37E ARG* 1.3 60.7 + - - +
38E GLY 4.0 5.9 + - - +
75E ASP 4.3 2.5 - - - -
76E ILE* 5.5 0.2 - - - -
23L SER* 4.4 26.9 - - - +
33L GLN* 5.6 3.6 - - - +
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Residues in contact with ARG 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E GLN 4.1 0.6 + - - -
36E VAL* 1.3 71.8 - - - +
38E GLY* 1.3 60.5 + - - +
74E VAL* 3.7 4.0 - - - +
75E ASP* 2.8 63.2 + - + +
76E ILE* 4.3 3.1 - - - +
77E VAL* 5.6 1.6 - - + +
33L GLN* 5.5 10.3 - - + -
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Residues in contact with GLY 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E VAL* 4.0 4.2 + - - +
37E ARG* 1.3 74.5 + - - +
39E PRO* 1.3 63.8 - - - -
40E ILE* 4.4 1.6 - - - -
73E LEU 5.1 0.4 - - - -
74E VAL* 5.1 0.7 - - - -
19L SER* 3.5 17.0 - - - +
23L SER* 3.4 29.3 - - - -
33L GLN* 5.7 3.8 - - - +
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Residues in contact with PRO 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E THR* 5.3 12.8 - - - -
38E GLY* 1.3 70.6 - - - -
40E ILE* 1.3 62.4 + - - +
72E ARG* 5.3 4.9 - - + -
73E LEU 3.3 17.7 - - - +
74E VAL* 3.7 16.3 - - + -
15L GLN 3.9 0.2 - - - +
18L TYR* 4.0 5.1 - - - +
19L SER* 3.3 28.5 + - - -
22L LEU* 5.1 12.5 - - + -
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Residues in contact with ILE 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E GLY* 4.4 1.9 - - - -
39E PRO* 1.3 75.8 - - - +
41E PRO* 1.3 65.6 - - - +
72E ARG* 3.8 5.0 - - - +
73E LEU* 3.2 30.2 + - + +
15L GLN* 4.1 25.6 - - + +
18L TYR* 5.2 0.7 - - - -
19L SER* 5.7 0.7 - - - -
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Residues in contact with PRO 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E ILE* 1.3 80.1 - - - +
42E LEU* 1.3 64.6 + - - +
71E LEU 4.3 7.6 - - - +
72E ARG* 4.7 3.4 - - + -
14L VAL 6.0 0.7 - - - +
15L GLN* 4.4 16.9 - - - +
18L TYR* 5.1 9.8 - - + -
80L VAL* 6.3 3.6 - - + -
114L PHE 5.8 3.8 - - - +
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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