Contacts of the strand formed by residues 31 - 37 (chain C) 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 TRP 31 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ARG 5.7 0.2 - - - -
30C TYR* 1.3 76.0 - - - +
32C MET* 1.3 60.2 + - - +
33C HIS* 4.1 9.4 - + + -
48C ALA* 3.7 21.8 - - + -
49C ILE* 3.6 24.9 - - - -
50C TYR* 3.4 48.8 - + + -
55C ASP* 3.7 30.7 - - - -
56C THR 4.8 1.1 - - - -
57C SER* 4.9 10.3 - - - -
96C ARG* 3.6 3.8 - - - +
97C ASP* 2.9 48.7 + - + +
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Residues in contact with MET 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C LEU* 4.4 5.2 - - + -
20C CYS* 4.1 21.3 - - - -
22C ALA* 5.0 1.1 - - + -
25C TYR* 3.2 27.6 - - + +
27C PHE* 4.3 18.8 - - + -
30C TYR* 5.0 3.8 - - + +
31C TRP* 1.3 74.4 - - - +
33C HIS* 1.3 61.4 + - - +
34C TRP* 3.9 11.6 - - - +
48C ALA* 3.2 3.4 - - - -
49C ILE* 3.1 44.3 + - + +
51C PRO* 5.1 1.3 - - + -
77C ALA* 3.9 24.0 - - + -
94C CYS* 4.2 0.9 - - + -
95C SER* 3.5 24.9 - - - +
96C ARG* 4.1 14.6 - - + +
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Residues in contact with HIS 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C TRP* 4.1 8.7 - + + -
32C MET* 1.3 74.8 - - - +
34C TRP* 1.3 64.9 + - - +
35C ILE* 4.0 14.8 - - + -
45C TRP* 2.8 30.9 - + - +
47C GLY 3.4 3.8 - - - -
48C ALA* 3.6 20.8 - - + +
93C TYR 3.8 0.2 - - - +
94C CYS* 3.2 5.9 - - - +
95C SER 2.7 40.7 + - - +
97C ASP* 2.6 46.0 + - + +
102C PHE* 3.6 23.2 - + + -
93D TYR* 3.8 19.8 - + - -
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Residues in contact with TRP 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C GLN* 4.1 13.9 - - - -
18C MET* 4.3 17.9 - - + -
19C SER* 4.1 9.0 - - - -
20C CYS* 3.7 26.2 - - + -
32C MET* 3.9 16.8 + - - +
33C HIS* 1.3 78.0 - - - +
35C ILE* 1.3 64.6 + - - +
45C TRP* 4.0 1.6 - - - -
46C ILE* 2.9 42.5 + - + +
47C GLY 3.0 10.9 + - - +
49C ILE* 4.7 2.8 - - - +
68C LEU* 3.7 29.1 - - + +
77C ALA* 3.6 32.0 - - + +
78C TYR 4.3 6.1 + - - -
79C MET* 3.5 38.8 - - + -
92C TYR* 4.8 2.7 - - + -
93C TYR 3.3 15.5 - - - -
94C CYS* 3.9 12.3 - - + -
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Residues in contact with ILE 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C HIS* 4.0 16.2 - - + +
34C TRP* 1.3 89.1 - - - +
36C LYS* 1.3 62.0 + - - +
43C LEU* 3.8 27.8 - - + -
44C GLU 3.4 23.1 - - - +
45C TRP* 4.6 6.3 - - + -
46C ILE* 4.1 3.8 - - - +
91C VAL 3.7 1.2 - - - +
92C TYR* 3.5 4.1 - - - +
93C TYR* 2.8 47.2 + - + +
95C SER* 4.1 8.3 - - - -
102C PHE* 4.4 4.5 - - + -
105C TRP* 3.7 30.7 - - + -
95D PHE* 4.0 21.3 - - + -
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Residues in contact with LYS 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C ILE* 1.3 74.0 - - - +
37C GLN* 1.3 63.9 + - - +
38C ARG* 3.6 24.0 - - - +
42C GLY 3.6 0.5 - - - +
43C LEU* 3.5 5.0 - - - -
44C GLU* 2.7 66.8 + - + +
46C ILE* 3.8 16.5 - - + +
61C LYS* 5.8 2.6 - - - +
62C PHE* 3.9 23.2 - - + -
87C GLU 2.8 29.3 + - - -
88C ASP* 4.2 7.4 + - - +
90C ALA* 3.8 9.2 - - + -
91C VAL 3.8 2.9 - - - -
92C TYR* 3.5 32.3 - - + +
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Residues in contact with GLN 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C LYS* 1.3 76.1 - - - +
38C ARG* 1.3 65.3 + - - +
39C PRO* 3.8 0.9 - - + +
40C GLY 5.9 0.4 - - - +
41C GLN 3.9 16.2 + - - +
42C GLY 3.7 5.8 - - - +
43C LEU* 3.5 21.7 - - + +
90C ALA* 3.6 3.7 - - - -
91C VAL* 3.0 43.2 + - + +
93C TYR* 3.8 15.9 + - + -
37D GLN* 2.8 44.1 + - - +
86D TYR* 3.7 13.7 + - - -
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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