Contacts of the strand formed by residues 35 - 41 (chain D) in PDB entry 3CWT
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 TYR 35 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16D LEU* 4.5 9.2 - - + +
19D LEU* 4.2 21.8 - - + +
28D GLU* 2.9 32.5 + - + +
29D THR 3.7 1.8 - - - -
30D VAL* 3.7 29.2 - - + -
34D TYR* 1.3 76.5 - - - +
36D ALA* 1.3 59.5 + - - +
37D ARG* 3.2 48.9 + - + -
48D VAL 4.1 0.6 - - - +
49D THR* 3.4 1.2 - - - +
50D ALA* 2.6 43.9 + - + +
52D PRO* 5.4 0.2 - - - +
78D MET* 4.9 7.6 - - - -
81D LEU* 4.7 13.8 - - + +
82D PHE* 3.8 33.2 - + + -
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Residues in contact with ALA 36 (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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28D GLU* 3.3 2.4 - - - +
29D THR* 2.8 32.8 + - - +
34D TYR* 4.1 17.9 - - + -
35D TYR* 1.3 79.0 - - - +
37D ARG* 1.3 66.2 + - - +
47D VAL* 4.9 1.8 - - + -
48D VAL 3.0 15.3 - - - +
49D THR* 3.9 12.3 - - - +
152D TYR* 3.6 19.3 - - + +
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Residues in contact with ARG 37 (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* 2.9 31.6 - - - +
28D GLU* 3.9 6.4 - - - +
35D TYR* 3.2 38.8 + - + +
36D ALA* 1.3 75.2 - - - +
38D SER* 1.3 84.7 + - - +
39D LEU* 4.3 3.5 - - + +
47D VAL* 3.5 3.6 - - - +
48D VAL* 3.0 35.8 + - + +
78D MET* 4.5 15.0 - - + -
81D LEU* 6.2 0.9 - - - -
111D VAL* 3.5 27.2 - - - +
115D GLU* 2.8 40.6 + - - -
119D ARG* 4.1 8.9 - - - +
152D TYR* 4.2 7.8 + - - -
155D PHE* 4.3 6.3 - - - +
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Residues in contact with SER 38 (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* 2.8 19.6 + - - +
37D ARG* 1.3 99.8 + - - +
39D LEU* 1.3 59.4 + - - +
46D GLY 3.6 10.3 - - - -
47D VAL* 4.3 4.3 - - - -
146D LEU* 4.3 5.8 - - - -
152D TYR* 4.2 4.1 - - - -
153D ILE 2.6 42.4 + - - -
154D CYS* 3.2 15.6 - - - -
155D PHE 3.9 1.4 + - - -
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Residues in contact with LEU 39 (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 ARG* 4.3 3.8 - - + +
38D SER* 1.3 82.2 - - - +
40D ALA* 1.3 66.5 + - - +
41D VAL* 4.8 2.0 - - + -
44D TYR 4.6 0.2 - - - -
45D ARG* 3.4 5.9 - - - +
46D GLY 3.1 29.8 + - - +
48D VAL* 3.3 33.9 - - + -
67D LEU* 3.8 8.5 - - + +
74D CYS* 3.8 27.8 - - + -
77D LYS* 4.3 15.3 - - + -
78D MET* 4.3 13.0 - - + -
111D VAL* 3.2 38.1 - - + -
154D CYS* 4.0 4.4 - - - +
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Residues in contact with ALA 40 (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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39D LEU* 1.3 79.4 - - - +
41D VAL* 1.3 65.2 - - - +
42D GLY 3.9 8.1 + - - +
44D TYR 3.4 4.0 - - - -
45D ARG* 4.1 19.3 - - + -
77D LYS* 4.3 10.9 - - - -
154D CYS* 4.3 14.8 - - + +
155D PHE 5.5 4.0 - - - +
157D THR* 5.8 7.6 - - + -
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Residues in contact with VAL 41 (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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39D LEU* 4.8 3.1 - - + -
40D ALA* 1.3 77.5 - - - +
42D GLY* 1.3 59.5 + - - +
43D GLU 3.0 8.5 + - - -
44D TYR* 3.0 25.6 + - - +
67D LEU* 5.1 1.6 - - + -
70D VAL* 3.8 28.9 - - + -
73D GLU* 4.0 31.0 - - + +
74D CYS* 4.0 26.0 - - - -
77D LYS* 4.3 20.9 - - + +
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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