Contacts of the strand formed by residues 64 - 67 (chain Q) 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 VAL 64 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32C PHE* 6.1 3.1 - - + -
33D TRP* 5.5 2.5 - - + +
98D LEU* 3.9 33.7 - - + -
33Q VAL* 3.5 9.0 - - - +
34Q ALA* 3.1 39.7 + - + +
35Q SER* 4.9 2.0 - - - +
63Q SER* 1.3 78.9 - - - +
65Q ILE* 1.3 72.3 + - - +
66Q LEU* 4.1 15.9 - - + -
82Q VAL* 4.8 0.7 - - + -
83Q PHE 3.3 8.3 - - - +
84Q GLN* 4.0 15.3 - - + -
85Q VAL* 4.0 0.4 - - - -
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Residues in contact with ILE 65 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31Q VAL* 3.9 15.7 - - + -
32Q LEU 3.5 10.3 - - - +
33Q VAL* 4.7 5.6 - - + -
52Q VAL* 4.1 30.1 - - + -
64Q VAL* 1.3 81.9 - - - +
66Q LEU* 1.3 74.7 + - - +
67Q LEU* 3.1 24.7 - - + -
82Q VAL* 3.4 5.2 - - - +
83Q PHE* 2.7 39.7 + - + +
85Q VAL* 4.5 10.1 - - + -
106Q LEU* 4.5 15.0 - - + -
108Q LEU* 4.2 21.3 - - + -
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Residues in contact with LEU 66 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C LEU* 4.6 9.4 - - + -
28C TYR* 4.6 23.3 - - + -
30C PHE* 3.1 38.4 - - + -
32C PHE* 5.6 3.8 - - + -
31Q VAL* 3.8 3.1 - - - -
32Q LEU* 3.1 47.7 + - + +
34Q ALA* 5.1 6.5 - - + -
64Q VAL* 4.1 16.4 - - + -
65Q ILE* 1.3 106.2 - - - +
67Q LEU* 1.3 62.5 + - - +
69Q ARG* 4.0 14.5 - - + +
72Q LEU* 5.8 0.4 - - + -
81Q GLN 3.7 4.9 - - - -
82Q VAL* 4.6 7.9 - - + -
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Residues in contact with LEU 67 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C PHE* 4.3 1.9 - - - -
28Q PRO 5.7 0.9 - - - +
30Q GLN 4.6 5.8 - - - +
31Q VAL* 4.1 12.1 - - + -
46Q LEU* 3.6 37.0 - - + -
65Q ILE* 3.1 37.7 - - + +
66Q LEU* 1.3 78.7 - - - +
68Q GLY* 1.3 65.4 + - - +
69Q ARG* 4.5 0.4 - - - -
79Q THR 3.9 0.2 - - - +
80Q GLY* 3.9 1.6 - - - -
81Q GLN* 3.3 37.6 + - + +
83Q PHE* 4.2 15.5 - - + -
108Q LEU* 5.1 3.1 - - + -
112Q ALA* 3.9 20.2 - - + -
118Q VAL* 4.1 13.2 - - + -
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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