Contacts of the strand formed by residues 38 - 46 (chain G) in PDB entry 2I9B
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 LEU 38 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C GLY* 3.7 42.8 - - - +
40C GLN* 3.9 7.6 - - + +
98C LYS 6.1 1.6 - - - +
29G VAL 3.6 1.8 - - - +
30G ARG* 3.5 4.3 - - - -
31G LEU* 2.5 62.3 + - + +
36G GLU* 5.9 4.3 - - + +
37G GLU* 1.3 79.2 - - - +
39G GLU* 1.3 61.0 + - - +
40G LEU* 4.9 7.2 - - + -
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Residues in contact with GLU 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C LYS* 5.2 9.9 + - - +
28G ILE* 4.1 9.8 - - + +
29G VAL 3.6 2.5 - - - -
30G ARG* 2.7 34.3 + - - +
37G GLU 4.3 1.3 + - - +
38G LEU* 1.3 77.4 - - - +
40G LEU* 1.3 69.6 + - - +
41G VAL* 3.5 28.0 + - + +
80G ASN* 5.8 0.3 + - - -
82G GLY 3.0 27.9 - - - +
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Residues in contact with LEU 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C ILE* 4.7 0.7 - - - -
29C HIS 3.4 25.4 - - - +
30C TRP* 3.9 19.1 - - + -
40C GLN* 4.4 35.2 - - + +
8G THR* 3.3 28.7 - - + +
27G THR 3.7 0.7 - - - +
28G ILE* 3.3 4.0 - - - +
29G VAL* 2.9 56.6 + - + +
31G LEU* 5.1 7.0 - - + -
38G LEU* 4.9 8.3 - - + +
39G GLU* 1.3 83.1 - - - +
41G VAL* 1.3 60.8 + - - +
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Residues in contact with VAL 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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6G CYS* 4.8 4.2 - - + +
7G LYS 3.6 6.4 - - - +
8G THR* 3.4 22.4 + - - -
10G GLY 5.5 0.3 + - - -
26G THR* 4.1 15.5 - - + -
27G THR 3.5 2.5 - - - -
28G ILE* 3.9 23.3 - - + -
39G GLU* 3.5 31.8 + - + +
40G LEU* 1.3 78.5 - - - +
42G GLU* 1.3 63.3 + - - +
43G LYS* 4.2 15.3 - - + -
79G GLY 5.9 1.1 - - - +
80G ASN 6.2 0.2 - - - +
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Residues in contact with GLU 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C SER 4.8 1.7 - - - +
27C ASN 4.8 1.4 - - - +
28C ILE* 3.3 44.5 + - + +
29C HIS* 6.1 0.9 - - - -
6G CYS* 3.4 16.9 - - - +
7G LYS* 4.8 2.3 - - - +
8G THR* 4.2 19.6 + - - +
25G ARG* 3.5 30.5 + - - +
26G THR* 3.5 0.5 - - - +
27G THR 2.7 38.2 + - - +
41G VAL* 1.3 75.3 - - - +
43G LYS* 1.3 65.6 - - - +
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Residues in contact with LYS 43 (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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4G MET* 3.5 17.8 - - - +
5G GLN* 3.1 2.3 - - - +
6G CYS* 2.9 51.0 + - - +
25G ARG* 3.8 8.8 + - - +
26G THR* 3.8 19.1 - - + +
41G VAL* 4.2 13.5 - - + -
42G GLU* 1.3 80.5 - - - +
44G SER* 1.3 68.3 + - - +
77G ASN* 2.9 55.5 + - - +
78G GLN* 3.5 16.6 + - - +
79G GLY 4.5 5.9 + - - +
80G ASN* 5.6 0.8 - - - +
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Residues in contact with SER 44 (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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3G CYS* 4.0 2.7 - - - -
4G MET 3.1 17.7 + - - -
5G GLN* 3.9 7.6 - - - -
15G GLU* 3.5 13.0 - - - -
24G CYS* 3.7 1.4 - - - -
25G ARG* 2.7 70.1 + - - +
43G LYS* 1.3 76.9 - - - +
45G CYS* 1.3 61.5 + - - +
77G ASN* 4.0 1.9 - - - +
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Residues in contact with CYS 45 (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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3G CYS* 2.0 42.6 - - - -
15G GLU* 3.2 24.4 + - - +
17G CYS* 2.0 50.9 - - - -
21G GLN* 3.4 10.2 + - - +
23G LEU 3.6 2.9 - - - +
25G ARG* 4.1 2.6 + - - +
44G SER* 1.3 88.9 + - - +
46G THR* 1.3 65.6 + - - +
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Residues in contact with THR 46 (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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26C SER* 5.4 2.0 + - - -
21G GLN* 3.2 21.4 - - - +
23G LEU* 2.8 35.7 + - + +
25G ARG* 4.1 25.0 - - + -
45G CYS* 1.3 78.6 - - - +
47G HIS* 1.3 66.7 + - - +
48G SER 3.5 1.0 + - - -
50G LYS* 3.0 42.6 + - + +
68G GLU* 4.9 1.7 + - - +
70G VAL* 4.1 6.5 - - + -
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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