Contacts of the strand formed by residues 33 - 40 (chain D) in PDB entry 43C9
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 ASN 33 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C ARG* 5.8 0.2 - - - +
31D ARG 5.6 0.8 - - - -
32D TYR* 1.3 72.8 - - - +
34D VAL* 1.3 60.8 + - - +
35D HIS* 3.8 9.8 + - - +
50D MET* 4.0 15.3 - - + +
51D ILE 3.9 4.0 - - - -
52D TRP* 3.1 38.6 - - - +
53D GLY* 3.0 23.2 + - - -
93D VAL 3.6 1.4 - - - +
94D SER* 3.0 4.2 - - - -
95D TYR* 2.8 50.6 + - + +
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Residues in contact with VAL 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D LEU* 5.7 0.9 - - + -
22D CYS* 4.5 1.6 - - - -
24D VAL* 5.4 1.8 - - + -
29D LEU* 4.3 13.2 - - + -
32D TYR* 4.5 6.7 - - + +
33D ASN* 1.3 73.9 - - - +
35D HIS* 1.3 66.0 + - - +
36D TRP* 5.4 1.3 - - - +
50D MET* 3.2 2.1 - - - -
51D ILE* 2.9 45.4 + - + +
71D LYS* 5.4 2.7 - - - +
78D ILE* 3.5 46.7 - - + +
92D CYS* 3.8 27.1 - - + -
93D VAL 3.3 7.6 - - - +
94D SER* 4.4 10.5 - - - -
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Residues in contact with HIS 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C GLN* 4.9 1.0 + - - -
91C HIS* 4.0 7.5 - + - -
96C ARG* 3.6 33.1 + - - -
33D ASN* 3.8 16.8 + - - +
34D VAL* 1.3 82.3 - - - +
36D TRP* 1.3 62.5 + - - +
37D VAL* 4.0 5.8 + - + +
47D TRP* 3.2 26.7 + - + +
49D GLY 3.3 8.1 - - - +
50D MET* 3.6 21.9 - - + +
91D TYR 3.7 0.5 - - - +
92D CYS* 3.0 8.5 - - - +
93D VAL* 2.7 42.6 + - + +
95D TYR* 3.5 32.5 - + - +
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Residues in contact with TRP 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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6D GLU* 4.2 6.1 - - + -
20D ILE* 3.7 30.5 - - + -
21D THR 4.0 0.2 - - - -
22D CYS* 3.5 28.3 - - + -
34D VAL 5.4 2.5 - - - -
35D HIS* 1.3 72.8 - - - +
37D VAL* 1.3 63.6 + - - +
47D TRP* 4.2 0.3 - - - -
48D LEU* 2.9 38.3 + - + -
49D GLY 3.0 14.0 + - - +
69D ILE* 3.7 25.1 - - + -
78D ILE* 3.4 36.5 - - + +
79D PHE* 2.8 29.5 + - - -
80D LEU* 3.6 26.0 - - + -
90D TYR* 5.0 3.4 - + + -
91D TYR* 3.2 34.5 - - - -
92D CYS* 3.9 11.7 - - + -
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Residues in contact with VAL 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C GLN* 5.1 0.9 - - - +
98C PHE* 4.1 15.7 - - + -
35D HIS* 4.6 5.4 - - + +
36D TRP* 1.3 78.2 - - - +
38D ARG* 1.3 62.3 + - - +
45D LEU* 3.8 28.7 - - + -
46D GLU 3.5 12.3 - - - +
47D TRP* 4.0 21.1 - - + -
48D LEU* 4.0 7.2 - - - +
90D TYR* 3.6 2.6 - - - +
91D TYR* 2.8 42.2 + - + +
93D VAL* 4.5 15.3 - - + -
103D TRP* 4.0 12.3 - - + -
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Residues in contact with ARG 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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37D VAL* 1.3 78.8 - - - +
39D GLN* 1.3 65.6 + - - +
40D SER* 5.7 0.2 - - - +
43D LYS* 4.0 20.6 - - - +
44D GLY 3.8 0.8 - - - +
45D LEU* 3.4 4.2 - - - +
46D GLU* 2.9 65.2 + - + +
48D LEU* 4.0 16.5 - - + +
63D LEU* 4.1 20.2 - - - +
82D MET* 3.8 10.9 - - - -
85D ASP* 4.7 3.4 + - - -
86D ASP* 3.2 28.2 + - - +
88D ALA* 3.8 16.6 - - + -
89D MET 3.1 12.6 - - - +
90D TYR* 3.1 41.1 + - + -
91D TYR* 4.6 1.1 - - - +
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Residues in contact with GLN 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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38C GLN* 2.6 46.9 + - - -
44C PRO* 4.2 0.5 - - - +
87C PHE* 4.2 6.5 - - - -
38D ARG* 1.3 79.9 - - - +
40D SER* 1.3 69.8 + - - +
44D GLY* 3.4 8.9 - - - +
45D LEU* 3.5 37.2 - - + +
88D ALA* 3.4 2.7 - - - +
89D MET* 2.9 34.8 + - + +
91D TYR* 3.8 20.9 + - + -
11F LEU* 4.3 3.3 - - - +
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Residues in contact with SER 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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38D ARG* 5.7 0.2 - - - +
39D GLN* 1.3 80.9 - - - +
41D PRO* 1.3 72.1 - - - +
43D LYS* 3.1 41.8 + - - +
44D GLY* 2.9 27.8 + - - -
87D SER 4.0 4.7 - - - -
88D ALA* 4.1 1.8 - - - -
11F LEU* 4.7 2.2 - - - -
112F SER* 3.2 25.4 + - - -
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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