Contacts of the strand formed by residues 34 - 41 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G PRO* 4.1 2.4 - - - +
28G ILE 3.8 0.2 - - - +
29G THR* 3.4 4.7 - - - -
30G SER* 3.0 29.0 + - - -
32G ASP* 2.7 31.4 + - - -
33G GLY* 1.3 80.7 - - - +
35G LEU* 1.3 60.3 + - - +
36G THR* 3.9 11.8 - - - +
52G SER* 4.2 13.2 - - - -
53G LEU 3.1 9.9 - - - -
54G ARG* 4.0 10.1 - - - +
59G LEU* 3.5 6.2 - - - +
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Residues in contact with LEU 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27G LEU* 4.5 13.9 - - + -
28G ILE 3.5 16.6 - - - +
29G THR* 3.7 21.5 - - + -
34G SER* 1.3 73.2 - - - +
36G THR* 1.3 62.5 + - - +
37G VAL* 4.1 5.1 + - + +
52G SER* 3.5 1.6 - - - -
53G LEU* 2.7 39.7 + - + +
59G LEU* 4.0 13.2 - - + -
62G CYS* 4.6 3.1 - - + -
72G ILE* 3.9 21.8 - - + -
74G VAL* 4.1 5.8 - - + -
84G VAL* 3.8 35.7 - - + -
86G LEU* 5.0 5.3 - - + +
92G PHE* 4.7 2.9 - - + -
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Residues in contact with THR 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G PRO* 3.7 31.9 - - + -
26G LEU 3.6 2.3 - - - +
27G LEU* 3.9 0.5 - - - -
28G ILE* 2.9 40.1 + - + +
34G SER* 3.9 10.5 - - - +
35G LEU* 1.3 75.5 - - - +
37G VAL* 1.3 61.1 + - - +
38G TYR* 2.8 31.0 + - + +
49G LEU* 4.6 6.6 - - - +
51G GLN 3.6 11.2 + - - -
52G SER* 3.9 11.9 - - - +
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Residues in contact with VAL 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G LEU* 4.2 19.3 - - + -
26G LEU 3.4 6.3 - - - +
27G LEU* 3.7 25.6 - - + -
35G LEU* 4.8 9.0 - - + +
36G THR* 1.3 75.5 - - - +
38G TYR* 1.3 74.5 + - - +
49G LEU* 4.2 0.5 - - - +
50G LEU* 2.9 34.9 + - + +
51G GLN* 3.1 21.6 + - + +
72G ILE* 4.8 1.1 - - + -
86G LEU* 4.2 33.2 - - + -
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Residues in contact with TYR 38 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G ILE* 3.2 32.0 - - + +
8G GLN* 2.3 35.4 + - - -
9G ALA* 3.5 11.3 - - - +
10G PRO* 3.8 7.8 - - - +
25G LEU* 3.3 13.0 - - - +
26G LEU* 3.0 44.6 + - + -
28G ILE* 3.9 24.9 - - + -
36G THR* 2.8 35.9 + - + -
37G VAL* 1.3 74.9 - - - +
39G LYS* 1.3 62.5 + - - +
47G VAL* 3.7 19.1 - - + -
48G ASP 3.5 4.9 - - - +
49G LEU* 3.8 25.4 - - + -
50G LEU* 4.6 1.6 - - - -
333G ILE* 4.2 0.6 - - + +
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Residues in contact with LYS 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G LYS 3.9 6.5 - - - -
24G SER* 3.4 23.6 + - - +
25G LEU* 4.0 13.9 - - + -
38G TYR* 1.3 75.9 - - - +
40G PHE* 1.3 81.0 + - - +
41G ASP* 4.7 8.4 - - + +
42G ILE* 5.9 1.0 - - - +
46G ASN* 4.1 0.7 + - - +
47G VAL* 3.2 3.4 - - - -
48G ASP* 2.8 33.8 + - + +
50G LEU* 3.6 29.4 - - + -
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Residues in contact with PHE 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G ILE* 4.1 10.5 - - + -
21G PRO* 4.9 4.9 - - + -
24G SER* 3.1 53.8 + - - -
25G LEU 3.4 18.6 - - - -
26G LEU* 4.4 10.8 - - + -
39G LYS* 1.3 96.7 + - - +
41G ASP* 1.3 64.7 + - - +
42G ILE* 4.2 22.7 - - + -
46G ASN 3.3 10.1 - - - +
47G VAL* 4.3 1.8 - - + -
303G SER* 5.5 2.0 - - - -
305G ASN* 6.3 0.2 - - + -
306G ILE* 3.6 32.8 - - + -
335G ILE* 3.9 21.8 - - + -
337G PHE* 4.3 8.3 - + + -
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Residues in contact with ASP 41 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39G LYS* 4.7 7.6 - - + +
40G PHE* 1.3 75.3 - - - +
42G ILE* 1.3 60.9 + - - +
43G GLN* 2.9 27.8 + - - +
44G ALA* 3.2 24.0 + - - +
45G LYS* 2.6 37.8 + - - -
46G ASN* 2.8 27.0 + - - +
337G PHE* 3.6 3.8 - - - -
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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