Contacts of the strand formed by residues 42 - 47 (chain D) in PDB entry 3CQ3
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 ARG 42 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D VAL 4.2 0.2 - - - +
38D VAL* 3.8 1.4 - - - +
39D GLU* 2.8 39.6 + - - +
40D PRO* 3.3 1.3 + - - +
41D PRO* 1.3 101.3 - - - +
43D ALA* 1.3 63.7 + - - +
74D VAL* 4.3 2.9 - - - +
76D GLU* 2.8 44.5 + - + +
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Residues in contact with ALA 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D VAL 3.3 8.5 - - - +
38D VAL* 4.2 16.4 - - + -
42D ARG* 1.3 76.8 - - - +
44D TYR* 1.3 61.9 + - - +
68D LEU* 4.6 12.1 - - + -
71D LEU* 5.1 0.4 - - + -
74D VAL* 3.7 22.9 - - + -
76D GLU 3.0 6.5 + - - +
77D VAL* 3.4 14.6 - - + -
78D GLU* 2.9 25.7 + - - +
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Residues in contact with TYR 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D ASP* 3.4 23.8 - - - -
36D LEU* 3.3 4.5 - - - +
37D VAL* 2.7 60.9 + - + +
43D ALA* 1.3 76.4 - - - +
45D VAL* 1.3 66.1 + - - +
46D ARG* 2.9 45.3 + - + +
68D LEU* 5.2 0.4 - - - -
78D GLU* 3.4 40.8 - - + +
80D GLU* 3.8 15.4 - - + +
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Residues in contact with VAL 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D LEU* 4.7 2.0 - - + -
33D ILE* 3.8 29.2 - - + -
35D ASP 3.3 13.0 - - - +
36D LEU* 4.0 14.8 - - + -
44D TYR* 1.3 79.6 - - - +
46D ARG* 1.3 67.2 + - - +
47D MSE 4.7 2.2 - - + -
64D VAL* 4.0 8.7 - - + -
68D LEU* 3.7 15.9 - - + -
78D GLU 3.0 4.6 + - - +
79D VAL* 3.6 35.3 - - + +
80D GLU* 2.8 27.0 + - - +
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Residues in contact with ARG 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D ILE* 3.7 1.2 - - - -
34D TYR* 2.7 48.9 + - + +
35D ASP* 2.9 48.3 + - + +
44D TYR* 2.9 32.7 + - + +
45D VAL* 1.3 73.1 - - - +
47D MSE 1.3 58.6 + - - +
80D GLU* 3.3 14.4 - - + +
82D THR* 3.7 27.6 - - + +
84D GLU 5.1 3.8 + - - -
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Residues in contact with MSE 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D VAL* 4.9 5.2 - - + -
32D LEU* 3.1 17.5 - - + +
33D ILE* 4.0 13.0 - - + -
34D TYR* 4.2 2.9 - - - +
45D VAL* 4.7 1.6 - - + -
46D ARG* 1.3 76.1 - - - +
48D THR* 1.3 78.7 + - - +
49D LEU* 4.2 10.8 - - + -
60D LEU* 4.2 22.9 - - + -
61D GLY* 4.1 10.5 - - - -
64D VAL* 3.6 36.6 - - + -
79D VAL* 3.8 24.2 - - + -
80D GLU 2.8 13.0 + - - +
81D VAL* 3.2 12.5 - - + -
82D THR* 2.8 30.9 + - - +
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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