Contacts of the strand formed by residues 32 - 37 (chain H) in PDB entry 3IU3
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 MET 32 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2H LEU* 4.0 13.5 - - + -
20H CYS* 4.1 18.6 - - - -
22H ALA* 4.4 4.3 - - + -
25H TYR* 3.3 26.0 - - - +
27H PHE* 3.7 24.9 - - + -
30H TYR 5.1 1.3 - - - +
31H TRP* 1.3 74.2 - - - +
33H HIS* 1.3 63.7 + - - +
34H TRP* 3.9 13.3 - - - +
48H ALA* 3.3 2.5 - - - -
49H ILE* 3.0 49.0 + - + +
51H PRO* 5.3 4.0 - - + -
77H ALA* 4.1 17.0 - - + -
94H CYS* 4.6 1.6 - - + -
95H SER 3.5 21.8 - - - +
96H ARG* 4.3 2.5 - - + -
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Residues in contact with HIS 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H TRP* 4.4 7.6 - + + -
32H MET* 1.3 76.5 + - - +
34H TRP* 1.3 64.0 + - - +
35H ILE* 3.9 16.6 - - + -
45H TRP* 2.8 30.7 + - - +
47H GLY 3.4 4.5 - - - +
48H ALA* 3.7 18.3 - - + +
93H TYR 3.8 0.2 - - - +
94H CYS* 3.2 5.4 - - - +
95H SER* 2.8 35.9 + - - +
97H ASP* 2.8 41.4 - - + +
102H PHE* 3.5 26.8 - + + -
42I LEU* 5.6 2.3 - - + +
93L TYR* 3.7 19.0 - + - -
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Residues in contact with TRP 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H GLN* 4.3 13.5 - - - -
18H MET* 4.0 26.2 - - + -
19H SER 4.0 4.7 - - - -
20H CYS* 3.7 25.6 - - + -
32H MET* 3.9 14.6 + - - +
33H HIS* 1.3 78.5 - - - +
35H ILE* 1.3 64.4 + - - +
45H TRP* 4.0 1.4 - - - -
46H ILE* 2.8 46.0 + - + +
47H GLY 3.0 10.3 + - - +
49H ILE* 4.6 2.2 - - - +
68H LEU* 3.5 30.9 - - + +
77H ALA* 3.6 31.0 - - + +
78H TYR 4.0 7.7 + - - -
79H MET* 3.2 36.3 - - + -
92H TYR* 4.7 3.8 - - + -
93H TYR 3.3 13.7 - - - -
94H CYS* 4.1 12.6 - - + -
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Residues in contact with ILE 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H HIS* 3.9 23.1 - - + -
34H TRP* 1.3 83.2 - - - +
36H LYS* 1.3 64.7 + - - +
43H LEU* 3.8 33.9 - - + -
44H GLU 3.3 12.3 - - - +
45H TRP* 4.6 4.5 - - + -
46H ILE* 3.9 3.6 - - - +
91H VAL 3.8 0.7 - - - +
92H TYR* 3.5 4.9 - - - -
93H TYR* 2.8 45.1 + - + +
95H SER* 4.1 8.7 - - - -
102H PHE* 4.2 7.4 - - + -
105H TRP* 3.9 26.7 - - + -
95L PHE* 3.9 21.8 - - + -
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Residues in contact with LYS 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35H ILE* 1.3 74.0 - - - +
37H GLN* 1.3 65.0 + - - +
38H ARG* 3.6 21.4 - - - +
42H GLY 3.5 0.7 - - - +
43H LEU* 3.3 5.5 - - - -
44H GLU* 2.7 64.0 + - + +
46H ILE* 3.8 17.6 - - + +
62H PHE* 3.7 30.0 - - + -
87H GLU 2.9 29.5 + - - -
88H ASP* 4.0 9.1 + - - +
90H ALA* 3.9 8.3 - - + -
91H VAL 3.8 3.1 - - - -
92H TYR* 3.8 25.1 + - + +
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Residues in contact with GLN 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36H LYS* 1.3 76.3 - - - +
38H ARG* 1.3 64.5 + - - +
39H PRO* 3.8 0.9 - - - +
40H GLY 5.9 0.2 - - - +
41H GLN 3.9 9.2 + - - +
42H GLY 3.4 13.5 - - - +
43H LEU* 3.4 18.9 - - + +
90H ALA* 3.7 3.7 - - - -
91H VAL* 3.0 44.7 + - + +
93H TYR* 3.5 19.5 + - + -
37L GLN* 2.6 45.4 + - - +
86L TYR* 3.7 11.3 + - - -
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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