Contacts of the strand formed by residues 34 - 41 (chain C) in PDB entry 2I3T
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 SER 34 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C PRO* 4.1 2.3 - - - +
28C ILE 3.8 0.2 - - - +
29C THR* 3.4 4.2 - - - -
30C SER* 3.0 29.8 + - - -
32C ASP* 2.7 30.0 + - - -
33C GLY* 1.3 79.9 - - - +
35C LEU* 1.3 58.7 + - - +
36C THR* 3.9 11.9 - - - +
52C SER* 4.2 13.7 - - - -
53C LEU 3.1 9.9 - - - -
54C ARG* 4.0 9.6 - - - +
59C LEU* 3.5 5.7 - - - +
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Residues in contact with LEU 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LEU* 4.5 13.7 - - + -
28C ILE 3.5 16.8 - - - +
29C THR* 3.7 21.8 - - + -
34C SER* 1.3 73.6 - - - +
36C THR* 1.3 62.7 + - - +
37C VAL* 4.1 5.5 + - + +
52C SER* 3.5 1.6 - - - -
53C LEU* 2.7 39.2 + - + +
59C LEU* 4.0 13.5 - - + -
62C CYS* 4.6 2.9 - - + -
72C ILE* 3.9 22.7 - - + -
74C VAL* 4.1 5.6 - - + -
84C VAL* 3.8 35.2 - - + -
86C LEU* 5.0 5.4 - - + -
92C PHE* 4.7 3.1 - - + -
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Residues in contact with THR 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C PRO* 3.7 32.8 - - + -
26C LEU 3.6 2.9 - - - +
27C LEU* 3.9 0.3 - - - -
28C ILE* 2.9 41.0 + - + +
34C SER* 3.9 10.3 - - - +
35C LEU* 1.3 76.4 - - - +
37C VAL* 1.3 61.2 + - - +
38C TYR* 2.8 31.5 + - + +
49C LEU* 4.6 6.0 - - - +
51C GLN 3.6 11.1 + - - -
52C SER* 3.9 12.1 - - - +
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Residues in contact with VAL 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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25C LEU* 4.2 20.2 - - + -
26C LEU 3.4 5.8 - - - +
27C LEU* 3.7 24.7 - - + -
35C LEU* 4.8 9.2 - - + +
36C THR* 1.3 75.3 - - - +
38C TYR* 1.3 73.8 + - - +
49C LEU* 4.2 0.5 - - - +
50C LEU* 2.9 34.6 + - + +
51C GLN* 3.1 22.0 + - + +
72C ILE* 4.8 1.8 - - + -
86C LEU* 4.3 33.0 - - + -
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Residues in contact with TYR 38 (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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6C ILE* 3.2 30.5 - - + +
8C GLN* 2.3 36.0 + - - -
9C ALA* 3.5 11.4 - - - +
10C PRO* 3.8 7.1 - - - +
25C LEU* 3.3 13.3 - - - +
26C LEU* 3.0 44.5 + - + -
28C ILE* 3.9 25.6 - - + -
36C THR* 2.8 33.9 + - - -
37C VAL* 1.3 74.8 - - - +
39C LYS* 1.3 61.9 + - - +
47C VAL* 3.7 19.1 - - + -
48C ASP 3.5 4.9 - - - -
49C LEU* 3.8 25.1 - - + -
50C LEU* 4.6 1.6 - - - -
333C ILE* 4.2 1.2 - - + +
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Residues in contact with LYS 39 (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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23C LYS 3.9 6.7 - - - -
24C SER* 3.4 26.7 + - - +
25C LEU* 4.0 11.4 - - + -
38C TYR* 1.3 75.7 - - - +
40C PHE* 1.3 79.5 + - - +
41C ASP* 4.7 9.0 - - + +
42C ILE* 5.9 0.8 - - - +
46C ASN* 5.5 0.7 + - - -
47C VAL* 3.2 2.8 - - - -
48C ASP* 2.8 34.5 + - + +
50C LEU* 3.6 28.9 - - + -
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Residues in contact with PHE 40 (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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19C ILE* 4.1 11.2 - - + -
21C PRO* 5.0 4.9 - - + -
24C SER* 3.1 52.1 + - - -
25C LEU 3.5 18.8 - - - -
26C LEU* 4.4 10.1 - - + -
39C LYS* 1.3 95.2 + - - +
41C ASP* 1.3 64.2 + - - +
42C ILE* 4.2 22.0 - - + -
46C ASN 3.3 10.3 - - - +
47C VAL* 4.1 2.5 - - + +
303C SER* 5.5 1.8 - - - -
305C ASN* 6.3 0.2 - - + -
306C ILE* 3.5 34.5 - - + -
335C ILE* 3.9 21.8 - - + -
337C PHE* 4.3 8.5 - + + -
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Residues in contact with ASP 41 (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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39C LYS* 4.7 7.0 - - - +
40C PHE* 1.3 75.3 - - - +
42C ILE* 1.3 62.1 + - - +
43C GLN* 2.9 26.3 + - - +
44C ALA* 3.2 24.6 + - - +
45C LYS* 2.6 37.6 + - - -
46C ASN* 2.9 25.4 + - - +
337C PHE* 3.6 3.6 - - - -
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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