Contacts of the strand formed by residues 45 - 51 (chain P) in PDB entry 3KYM
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 45 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36O TYR* 5.2 3.4 - - + -
38O GLN* 4.7 1.1 - - - +
44O PRO* 4.1 29.4 - - + -
87O TYR* 3.7 33.8 - - + -
98O PHE* 3.6 53.6 - - + +
37P VAL* 4.5 7.0 - - + -
38P ARG 3.6 4.9 - - - +
39P GLN* 3.3 31.0 - - + +
44P GLY* 1.3 73.6 - - - -
46P GLU* 1.3 67.7 + - - +
95P TYR* 4.6 8.5 - - + -
109P TRP* 4.3 5.4 - - + -
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Residues in contact with GLU 46 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98O PHE* 3.7 3.3 - - - -
37P VAL* 4.0 0.9 - - - -
38P ARG* 2.8 76.8 + - + +
39P GLN* 5.4 0.4 - - - -
40P ALA 6.0 0.4 - - - +
44P GLY 4.7 2.9 - - - +
45P LEU* 1.3 79.3 - - - +
47P TRP* 1.3 92.8 + - - +
63P SER* 5.1 11.1 + - - -
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Residues in contact with TRP 47 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94O TRP* 4.4 24.7 - + - -
95O PRO* 4.7 12.6 - - + -
96O LEU* 3.7 35.1 - - + +
97O THR* 5.4 1.1 - - - -
98O PHE* 3.2 23.8 - - + -
35P PHE* 3.4 40.9 - + - -
36P TRP 4.4 1.3 - - - -
37P VAL* 4.1 7.2 - - - -
46P GLU* 1.3 91.1 + - - +
48P VAL* 1.3 78.5 + - - +
49P SER* 3.5 10.3 + - - -
50P TRP* 4.4 1.5 - - - +
60P TYR 4.7 0.9 - - - -
61P ALA* 3.8 7.6 - - + -
62P ASP* 3.2 46.6 - - + +
63P SER* 5.9 0.7 - - - -
106P PHE* 4.1 13.2 - + + -
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Residues in contact with VAL 48 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36P TRP* 3.1 20.9 + - + +
37P VAL 3.7 2.5 - - - -
38P ARG* 3.4 55.9 - - + +
46P GLU 3.5 1.1 - - - +
47P TRP* 1.3 88.9 - - - +
49P SER* 1.3 63.7 + - - +
61P ALA* 2.4 30.0 - - + +
62P ASP 4.7 3.4 - - - +
68P PHE* 4.3 24.5 - - + -
81P LEU* 5.3 3.4 - - + -
94P TYR* 5.0 4.3 - - + -
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Residues in contact with SER 49 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35P PHE* 3.2 20.6 - - - -
36P TRP* 3.2 22.0 + - - +
47P TRP* 3.8 3.4 - - - -
48P VAL* 1.3 88.9 - - - +
50P TRP* 1.3 61.5 + - - +
60P TYR* 4.8 0.6 - - - +
61P ALA* 3.3 14.9 + - - +
68P PHE* 5.0 5.5 + - - +
70P ILE* 3.5 33.5 + - - +
81P LEU* 3.8 15.6 - - - +
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Residues in contact with TRP 50 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D SER* 5.8 6.7 - - - -
93O LYS 6.0 0.9 - - - -
94O TRP* 3.8 36.1 - + - +
33P PRO* 3.5 15.4 - - + +
34P MET 3.3 13.2 - - - -
35P PHE* 3.5 34.8 - + + -
47P TRP* 4.4 2.7 - - + +
49P SER* 1.3 76.4 - - - +
51P ILE* 1.3 70.6 + - - +
52P GLY* 3.7 14.6 - - - -
53P PRO* 4.8 3.4 - - + -
59P LYS* 3.0 54.1 - - + +
60P TYR 3.3 29.0 + - - +
61P ALA* 4.7 0.2 - - - +
70P ILE* 3.7 4.3 - - - +
104P TRP* 3.3 43.3 - + - -
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Residues in contact with ILE 51 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33P PRO* 3.1 7.1 - - - +
34P MET 3.0 30.2 + - - +
50P TRP* 1.3 74.9 - - - +
52P GLY* 1.3 77.6 + - - +
56P GLY* 4.3 19.7 - - - +
58P THR* 5.1 1.1 - - - +
59P LYS* 3.6 30.5 - - + +
60P TYR* 5.6 1.6 - - + -
70P ILE* 3.5 48.9 - - + +
71P SER* 4.4 5.4 - - - +
72P ARG* 3.4 32.8 - - + +
79P LEU* 4.7 4.5 - - + -
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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