Contacts of the strand formed by residues 15 - 23 (chain I) in PDB entry 2QME
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 SER 15 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A THR 5.5 2.9 - - - -
42A ALA* 3.5 4.7 - - - +
43A ASN* 2.8 37.6 + - - +
13I LEU 5.0 1.3 + - - -
14I PRO* 1.3 76.1 - - - +
16I ASP* 1.3 84.4 + - - +
17I PHE* 3.3 3.6 + - - -
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Residues in contact with ASP 16 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A SER* 3.5 8.7 + - - +
42A ALA* 4.0 2.3 - - - -
43A ASN* 3.0 31.8 + - - +
15I SER* 1.3 91.4 + - - +
17I PHE* 1.3 68.2 + - - +
18I GLU* 3.2 5.9 + - - +
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Residues in contact with PHE 17 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ILE* 4.2 9.6 - - + -
24A THR* 3.3 47.1 - - - +
25A THR* 3.6 21.3 - - + -
40A TYR* 3.8 29.6 - + + -
41A SER 3.3 9.0 - - - -
42A ALA* 4.6 2.2 - - - +
15I SER 3.3 4.1 - - - -
16I ASP* 1.3 77.9 - - - +
18I GLU* 1.3 62.4 + - - +
19I HIS* 3.9 32.1 - + + -
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Residues in contact with GLU 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A TYR* 3.3 5.5 - - - +
41A SER* 2.9 41.2 + - - +
16I ASP 4.3 4.5 - - - +
17I PHE* 1.3 81.5 - - - +
19I HIS* 1.3 64.9 + - - +
20I THR* 3.2 27.7 + - + +
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Residues in contact with HIS 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ASP* 2.8 31.4 + - - -
39A ASN 3.6 8.3 - - - -
40A TYR* 3.6 21.1 - + - -
17I PHE* 3.9 19.8 - - + -
18I GLU* 1.3 74.6 - - - +
20I THR* 1.3 63.2 + - - +
21I ILE 3.2 21.2 + - - -
22I HIS* 3.7 17.0 - + + +
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Residues in contact with THR 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ASN* 2.3 40.8 + - - +
41A SER* 3.7 26.5 - - - +
18I GLU* 3.2 33.9 - - - +
19I HIS* 1.3 75.0 - - - +
21I ILE* 1.3 70.5 + - - +
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Residues in contact with ILE 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A PHE* 3.9 27.1 - - + -
38A ASP* 3.3 1.6 - - - -
39A ASN* 3.0 44.3 + - + +
56A TRP* 5.9 6.3 - - + -
19I HIS* 3.2 14.1 + - - -
20I THR* 1.3 90.7 + - - +
22I HIS* 1.3 63.7 + - - +
23I VAL* 4.1 17.0 - - + -
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Residues in contact with HIS 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ILE* 6.5 0.9 - - + -
36A VAL 6.3 0.2 - - - -
38A ASP* 2.6 28.6 + - - +
19I HIS* 3.7 16.5 + + + +
21I ILE* 1.3 75.4 - - - +
23I VAL* 1.3 86.2 + - - +
24I GLY* 3.9 9.4 + - - -
33I THR* 3.8 13.1 - - - +
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Residues in contact with VAL 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A VAL* 3.5 24.6 + - + +
37A PHE* 2.9 45.7 + - + +
38A ASP* 4.7 0.2 - - - +
67A LEU* 5.8 1.3 - - + -
21I ILE* 4.1 9.6 - - + -
22I HIS* 1.3 91.5 - - - +
24I GLY* 1.3 71.7 + - - +
32I PHE* 3.7 25.4 - - + -
33I THR 3.5 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