Contacts of the strand formed by residues 33 - 40 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A ARG* 6.1 0.4 - - - +
32B TYR* 1.3 73.6 - - - +
34B VAL* 1.3 61.7 + - - +
35B HIS* 3.7 9.3 + - - +
50B MET* 4.1 14.3 - - + +
51B ILE 3.8 3.1 - - - +
52B TRP* 2.9 41.7 - - - -
53B GLY* 2.7 31.0 + - - -
93B VAL 3.5 1.4 - - - +
94B SER* 3.1 3.8 - - - -
95B TYR* 2.8 45.5 + - + +
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Residues in contact with VAL 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 5.2 0.9 - - + -
22B CYS* 4.7 1.6 - - - -
24B VAL* 5.3 1.8 - - + -
29B LEU* 4.3 15.5 - - + -
32B TYR* 4.5 6.5 - - + +
33B ASN* 1.3 76.3 - - - +
35B HIS* 1.3 74.7 + - - +
36B TRP* 5.3 0.9 - - - +
50B MET* 3.2 1.6 - - - -
51B ILE* 2.9 43.9 + - + +
71B LYS* 6.3 1.6 - - + -
78B ILE* 3.9 43.7 - - + +
92B CYS* 4.0 17.0 - - + -
93B VAL 3.3 8.5 - - - +
94B SER* 4.1 13.5 - - - +
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Residues in contact with HIS 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLN* 5.1 0.6 + - - -
91A HIS* 4.2 4.4 - - - -
96A ARG* 3.4 36.6 + - - -
33B ASN* 3.7 17.3 + - - +
34B VAL* 1.3 82.2 - - - +
36B TRP* 1.3 64.9 + - - +
37B VAL* 4.6 6.1 - - + -
47B TRP* 3.1 24.2 + - + +
49B GLY 3.4 8.7 - - - +
50B MET* 3.7 24.0 - - + +
91B TYR 3.8 0.2 - - - +
92B CYS* 3.1 9.0 - - - +
93B VAL* 2.8 40.6 + - + +
95B TYR* 3.5 27.6 - + + +
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Residues in contact with TRP 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B GLU* 4.5 5.2 - - + -
20B ILE* 3.8 30.3 - - + -
21B THR 4.2 0.4 - - - -
22B CYS* 3.7 30.1 - - + -
34B VAL 5.3 1.1 - - - -
35B HIS* 1.3 75.6 - - - +
37B VAL* 1.3 61.8 + - - +
47B TRP* 4.1 0.7 - - - -
48B LEU* 2.8 46.9 + - + -
49B GLY 3.0 13.6 + - - +
69B ILE* 3.8 31.0 - - + -
78B ILE* 3.3 41.6 - - + +
79B PHE 3.4 9.9 + - - -
80B LEU* 3.6 31.4 - - + -
90B TYR* 5.2 1.6 - + + -
91B TYR* 3.2 32.1 - - - -
92B CYS* 3.9 11.9 - - + -
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Residues in contact with VAL 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLN* 5.1 0.9 - - - +
98A PHE* 3.8 21.5 - - + -
35B HIS* 4.6 7.0 - - + -
36B TRP* 1.3 82.9 - - - +
38B ARG* 1.3 66.4 + - - +
45B LEU* 3.7 29.4 - - + -
46B GLU 3.3 12.1 - - - +
47B TRP* 4.0 18.4 - - + -
48B LEU* 4.1 6.2 - - - +
90B TYR* 3.7 2.4 - - - +
91B TYR* 2.9 37.3 + - + +
93B VAL* 4.9 9.2 - - + -
103B TRP* 4.3 13.5 - - + -
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Residues in contact with ARG 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B VAL* 1.3 81.7 - - - +
39B GLN* 1.3 64.7 + - - +
40B SER* 5.9 0.7 - - - +
43B LYS* 3.3 23.7 - - - +
44B GLY 3.5 0.9 - - - +
45B LEU* 3.5 1.9 - - - -
46B GLU* 2.7 66.3 + - + +
48B LEU* 4.1 16.2 - - + +
63B LEU* 4.4 17.3 - - - +
82B MET* 3.3 13.7 - - - +
86B ASP* 3.3 25.1 + - - +
88B ALA* 3.8 13.7 - - + -
89B MET 3.2 11.0 - - - +
90B TYR* 3.2 40.6 + - + -
91B TYR* 5.0 1.3 - - - -
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Residues in contact with GLN 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLN* 2.8 45.8 + - - +
44A PRO* 4.4 0.3 - - - +
87A PHE* 4.0 6.3 - - - -
38B ARG* 1.3 77.7 - - - +
40B SER* 1.3 68.0 + - - +
44B GLY* 3.3 13.2 - - - +
45B LEU* 3.8 32.5 - - + +
88B ALA* 3.4 3.3 - - - +
89B MET* 2.7 42.9 + - + +
91B TYR* 3.9 18.7 + - + -
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Residues in contact with SER 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ARG* 5.9 1.0 - - - +
39B GLN* 1.3 80.1 - - - +
41B PRO* 1.3 70.7 - - - +
42B GLY 4.2 1.1 - - - -
43B LYS* 3.0 41.6 + - - +
44B GLY* 2.8 27.8 + - - -
87B SER 4.0 20.0 - - - -
88B ALA* 4.3 2.5 - - - +
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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
------------------------------------------------------------
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