Contacts of the strand formed by residues 33 - 40 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31F ARG 5.6 1.5 + - - -
32F TYR* 1.3 73.2 - - - +
34F VAL* 1.3 59.2 + - - +
35F HIS* 4.1 6.2 + - + +
50F MET* 3.8 17.9 - - + -
51F ILE 3.7 5.6 - - - +
52F TRP* 3.0 39.3 - - - -
53F GLY* 2.7 28.2 + - - -
93F VAL 3.8 0.9 - - - +
94F SER* 3.3 3.8 - - - -
95F TYR* 2.9 45.0 + - + +
96F GLY* 5.7 1.2 - - - -
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Residues in contact with VAL 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F LEU* 5.8 0.7 - - + -
22F CYS* 4.6 1.6 - - - -
24F VAL* 5.4 2.2 - - + -
29F LEU* 4.3 16.6 - - + -
32F TYR* 4.3 6.3 - - + +
33F ASN* 1.3 75.5 - - - +
35F HIS* 1.3 66.2 + - - +
36F TRP* 5.2 1.4 - - - +
50F MET* 3.3 2.4 - - - -
51F ILE* 3.0 41.2 + - + +
71F LYS* 6.2 1.3 - - + -
78F ILE* 3.8 46.7 - - + +
92F CYS* 4.0 25.6 - - + -
93F VAL 3.5 8.3 - - - +
94F SER* 4.3 12.8 - - - +
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Residues in contact with HIS 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89E GLN* 4.6 3.4 + - - -
91E HIS* 4.1 3.6 - - - -
96E ARG* 3.6 36.8 + - - -
33F ASN* 4.2 5.2 - - - +
34F VAL* 1.3 77.0 - - - +
36F TRP* 1.3 63.2 + - - +
37F VAL* 4.0 7.2 + - + +
47F TRP* 3.1 23.5 + - - +
49F GLY 3.5 6.1 - - - +
50F MET* 3.1 34.0 - - + +
92F CYS* 3.0 8.5 - - - +
93F VAL* 2.8 48.2 + - + +
95F TYR* 3.9 33.4 - + - +
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Residues in contact with TRP 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F GLU* 4.2 4.7 - - + -
20F ILE* 3.3 33.4 - - + -
21F THR 4.2 0.2 - - - -
22F CYS* 3.6 21.3 - - + -
34F VAL 5.2 2.5 - - - -
35F HIS* 1.3 72.9 - - - +
37F VAL* 1.3 64.8 + - - +
47F TRP* 4.6 0.2 - - - -
48F LEU* 2.9 42.4 + - + +
49F GLY 2.8 17.9 + - - +
69F ILE* 3.9 24.0 - - + -
78F ILE* 3.6 34.8 - - + +
79F PHE 3.0 22.8 + - - -
80F LEU* 3.3 33.2 - - + +
90F TYR* 4.8 2.0 - - + -
91F TYR* 3.0 39.0 - - - -
92F CYS* 3.7 7.6 - - + -
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Residues in contact with VAL 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E GLN* 5.2 0.4 - - - +
98E PHE* 4.1 22.0 - - + -
35F HIS* 4.4 6.5 - - + +
36F TRP* 1.3 80.1 - - - +
38F ARG* 1.3 80.6 + - - +
45F LEU* 4.3 9.9 - - + -
46F GLU 3.2 21.1 - - - +
47F TRP* 4.1 21.8 - - + -
48F LEU* 4.4 4.3 - - - +
90F TYR* 3.6 5.4 - - - +
91F TYR* 2.8 37.6 + - + +
93F VAL* 4.4 20.2 - - + -
103F TRP* 4.4 7.4 - - + -
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Residues in contact with ARG 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F VAL* 1.3 81.9 - - - +
39F GLN* 1.3 64.0 + - - +
40F SER* 5.5 0.2 - - - +
43F LYS* 4.3 13.2 - - - +
44F GLY 3.7 1.6 - - - +
45F LEU* 3.8 1.4 - - - -
46F GLU* 2.7 66.6 + - + +
48F LEU* 4.1 12.4 - - + +
63F LEU* 4.4 19.6 - - - +
66F ARG* 5.7 0.2 - - - +
82F MET* 3.3 10.9 - - - +
85F ASP* 4.9 1.4 + - - +
86F ASP* 2.9 33.3 + - - +
88F ALA* 3.9 14.8 - - + -
89F MET 3.2 9.9 - - - +
90F TYR* 2.7 53.6 + - + -
91F TYR* 4.8 1.1 - - - -
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Residues in contact with GLN 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D LEU* 3.8 5.1 - - - +
38E GLN* 3.1 40.6 + - - -
44E PRO* 4.4 0.9 - - - +
87E PHE* 4.3 7.3 - - - -
38F ARG* 1.3 77.1 - - - +
40F SER* 1.3 70.5 + - - +
44F GLY* 3.6 11.8 - - - +
45F LEU* 3.8 29.9 - - + +
88F ALA* 3.6 0.7 - - - -
89F MET* 2.8 47.1 + - + +
91F TYR* 3.8 21.6 + - + -
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Residues in contact with SER 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D LEU* 4.6 0.7 - - - -
112D SER* 3.2 29.2 - - - -
38F ARG* 5.5 0.2 - - - +
39F GLN* 1.3 75.8 + - - +
41F PRO* 1.3 68.4 - - - +
43F LYS* 3.6 18.8 + - - +
44F GLY* 2.7 34.0 + - - -
87F SER 3.3 7.6 + - - -
88F ALA* 3.0 28.1 - - - +
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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