Contacts of the strand formed by residues 46 - 49 (chain K) in PDB entry 3QUM
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 46 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37K VAL* 3.2 7.1 - - - +
38K LYS* 2.8 52.2 + - + +
40K ARG* 5.8 2.4 - - - +
44K GLY 4.6 3.4 - - - +
45K LEU* 1.3 77.4 - - - +
47K TRP* 1.3 63.2 + - - +
60K ASN* 5.5 1.1 - - - +
62K LYS* 4.9 13.9 - - - +
63K PHE* 3.9 31.6 - - + -
98M PHE* 4.2 4.7 - - - -
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Residues in contact with TRP 47 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35K ASN* 3.6 23.9 + - + +
36K TRP 4.0 7.9 - - - -
37K VAL* 4.3 6.7 - - + +
46K GLU* 1.3 77.6 - - - +
48K ILE* 1.3 71.5 + - - +
49K GLY* 3.1 28.3 + - - -
50K ARG* 3.7 17.7 - - - -
58K LYS 3.1 22.4 - - - -
59K TYR 3.8 13.5 - - - -
60K ASN* 3.1 36.1 + - + +
63K PHE* 3.3 12.8 - - - -
100K PHE* 4.1 20.0 + - - -
94M TYR* 3.7 26.9 - + - -
95M PRO* 4.4 0.2 - - + -
96M VAL* 3.5 50.6 + - + +
98M PHE* 4.3 9.2 - + + -
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Residues in contact with ILE 48 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36K TRP* 3.0 27.8 + - + +
37K VAL 4.1 0.9 - - - -
38K LYS* 3.9 17.7 - - + +
47K TRP* 1.3 85.0 - - - +
49K GLY* 1.3 62.3 + - - +
59K TYR* 3.6 6.9 - - + +
60K ASN* 3.0 25.5 + - - +
63K PHE* 3.6 39.4 - - + +
67K ALA* 4.6 14.4 - - + -
69K LEU* 4.7 7.0 - - + -
80K MET* 4.0 16.4 - - + -
82K LEU* 6.1 0.4 - - + -
90K TYR* 3.9 31.6 - - + -
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Residues in contact with GLY 49 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34K MET 4.0 0.2 - - - +
35K ASN* 3.3 4.3 - - - -
36K TRP* 3.2 24.5 + - - -
47K TRP* 3.1 24.8 - - - -
48K ILE* 1.3 84.0 - - - +
50K ARG* 1.3 61.3 + - - +
58K LYS 3.7 5.2 - - - -
59K TYR* 4.1 4.5 - - - -
69K LEU* 3.8 10.1 - - - -
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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