Contacts of the strand formed by residues 38 - 44 (chain I) in PDB entry 3KL8
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 GLU 38 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29I ARG* 2.8 39.4 + - - +
30I CYS 3.5 5.8 - - - +
31I VAL* 3.9 9.0 - - + -
36I GLY 3.5 4.5 + - - +
37I LEU* 1.3 73.1 - - - +
39I PHE* 1.3 74.8 + - - +
91I LEU* 3.7 24.8 + - + +
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Residues in contact with PHE 39 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13I TYR* 4.1 19.5 - + - -
29I ARG* 3.2 25.6 - - - +
30I CYS* 2.8 24.6 + - - +
32I HIS* 4.8 7.0 - + + -
35I THR* 5.7 0.4 - - - -
37I LEU* 3.4 37.4 + - + -
38I GLU* 1.3 87.5 - - - +
40I ALA* 1.3 60.8 + - - +
76I HIS* 3.7 30.7 - + + -
88I VAL* 3.5 28.0 - - + -
89I PHE 3.6 14.6 - - - +
90I ASP* 4.5 7.2 - - - -
91I LEU* 3.8 11.3 - - - +
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Residues in contact with ALA 40 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I VAL* 4.5 12.8 - - + -
28I ARG 3.9 5.6 - - - +
29I ARG* 4.5 0.4 - - - +
30I CYS* 4.5 1.3 - - - -
39I PHE* 1.3 76.1 - - - +
41I ALA* 1.3 59.1 + - - +
42I LYS 3.9 0.8 + - - -
87I LEU 3.4 2.1 - - - +
88I VAL* 4.6 0.2 - - - -
89I PHE* 2.6 41.7 + - + +
90I ASP 3.8 17.9 - - - +
91I LEU* 3.8 16.6 - - + +
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Residues in contact with ALA 41 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9I PHE* 4.3 21.1 - - + -
27I VAL* 3.8 2.5 - - - -
28I ARG 2.8 31.2 + - - +
30I CYS* 3.6 23.3 - - + -
40I ALA* 1.3 72.7 - - - +
42I LYS* 1.3 63.7 + - - +
43I ILE* 3.3 17.9 + - + +
86I TYR* 5.0 2.0 - - + -
87I LEU 3.3 8.1 - - - +
88I VAL* 4.7 4.7 - - + -
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Residues in contact with LYS 42 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22I GLY 5.7 1.3 - - - -
25I SER* 4.2 13.0 - - - +
26I VAL 4.2 1.8 - - - +
27I VAL* 3.4 30.8 - - + +
40I ALA 3.9 1.6 + - - -
41I ALA* 1.3 72.1 - - - +
43I ILE* 1.3 62.2 + - - +
44I ILE* 4.1 17.5 - - + -
60I GLU* 5.4 5.1 + - - -
85I HIS 3.3 4.7 - - - +
86I TYR* 3.4 1.9 - - - -
87I LEU* 2.9 62.3 + - + +
89I PHE* 4.3 12.6 - - + -
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Residues in contact with ILE 43 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9I PHE* 5.4 1.6 - - + -
15I VAL* 5.3 7.2 - - + -
25I SER 3.3 11.0 + - - -
26I VAL* 2.7 35.3 + - + +
28I ARG* 4.1 26.9 - - + -
41I ALA* 3.3 20.9 - - + +
42I LYS* 1.3 74.3 - - - +
44I ILE* 1.3 63.2 + - - +
45I ASN* 5.6 0.2 - - - +
84I PHE* 4.0 27.1 - - + -
85I HIS 3.2 8.7 - - - +
86I TYR* 3.7 32.5 - - + +
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Residues in contact with ILE 44 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25I SER* 3.6 19.3 - - - +
42I LYS* 4.2 21.5 - - + -
43I ILE* 1.3 76.7 - - - +
45I ASN* 1.3 65.9 + - - +
57I LEU* 4.0 34.3 - - + -
84I PHE* 3.1 12.6 - - - +
85I HIS* 2.8 73.8 + - + +
87I LEU* 5.0 7.2 - - + -
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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