Contacts of the strand formed by residues 45 - 51 (chain B) in PDB entry 3KDM
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A TYR* 5.0 2.0 - - + -
40A GLN* 4.4 0.2 - - - +
46A PRO* 3.5 36.3 - - + -
89A TYR* 3.6 40.4 - - + -
102A PHE* 3.3 52.8 - - + +
103A GLY 4.9 1.4 - - - +
37B VAL* 4.1 13.5 - - + -
38B ARG 3.7 1.1 - - - -
39B GLN* 3.6 31.4 - - + +
44B GLY* 1.3 73.2 - - - -
46B GLU* 1.3 60.4 + - - +
95B TYR* 4.5 4.5 - - + -
112B TRP* 4.7 1.3 - - + -
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Residues in contact with GLU 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A PHE* 3.9 3.6 - - - -
37B VAL* 3.3 1.4 - - - +
38B ARG* 2.7 79.2 + - + +
44B GLY 4.9 2.0 - - - +
45B LEU* 1.3 74.8 - - - +
47B TRP* 1.3 72.1 + - - +
48B VAL* 3.6 1.1 + - - +
61B ALA* 4.1 3.6 - - + +
63B SER* 2.9 30.7 + - - -
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Residues in contact with TRP 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A THR* 5.8 2.2 - - + -
99A PRO* 3.7 24.5 - - + -
100A TYR* 3.7 39.9 - + + +
101A VAL* 5.5 0.9 - - - -
102A PHE* 3.5 16.6 - - + -
35B SER* 3.1 29.1 + - - -
36B TRP 3.6 1.6 - - - -
37B VAL* 4.1 6.5 - - + -
46B GLU* 1.3 79.3 - - - +
48B VAL* 1.3 61.4 + - - +
49B SER* 3.2 27.9 + - - -
50B ALA* 3.6 4.5 - - + -
59B TYR* 3.6 30.5 - - + -
60B TYR* 3.7 3.4 - - - -
61B ALA* 3.3 45.8 - - + +
226B TES 3.5 35.1 - - + +
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Residues in contact with VAL 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B TRP* 2.9 24.3 + - + +
37B VAL 4.0 1.6 - - - -
38B ARG* 3.6 52.0 - - + +
46B GLU* 3.7 1.1 - - + +
47B TRP* 1.3 82.5 - - - +
49B SER* 1.3 74.2 + - - +
60B TYR* 3.5 1.7 - - - -
61B ALA* 3.4 22.3 + - - -
64B VAL* 3.5 16.4 - - + +
68B PHE* 4.0 26.7 - - + -
81B LEU* 4.4 5.4 - - + -
94B TYR* 4.5 3.6 - - + -
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Residues in contact with SER 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B SER* 3.1 8.8 + - - -
36B TRP* 2.9 26.0 + - - -
47B TRP* 3.5 7.4 - - - -
48B VAL* 1.3 94.8 - - - +
50B ALA* 1.3 61.6 + - - +
59B TYR 2.9 19.1 + - - -
60B TYR* 3.7 17.6 - - - -
70B ILE* 3.7 26.0 - - - +
81B LEU* 4.6 7.2 - - - -
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Residues in contact with ALA 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ALA* 5.6 0.2 - - + -
34B MET 2.7 18.4 - - - +
35B SER* 4.3 0.2 - - - -
47B TRP* 3.6 12.3 - - + +
49B SER* 1.3 75.7 + - - +
51B ILE* 1.3 61.8 + - - +
57B SER 3.6 0.2 - - - +
58B THR* 3.6 23.2 - - - -
59B TYR* 3.7 8.7 + - - +
70B ILE* 3.8 8.3 - - - +
226B TES 3.9 43.5 - - + -
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Residues in contact with ILE 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ALA* 3.0 7.7 - - - -
34B MET* 2.6 55.7 + - + -
50B ALA* 1.3 76.8 - - - +
52B SER* 1.3 66.7 - - - +
55B GLY 3.5 23.3 - - - +
57B SER 3.5 10.1 - - - +
58B THR* 5.1 1.8 - - + -
59B TYR* 5.9 0.4 - - - -
70B ILE* 3.4 28.0 - - + +
71B SER* 3.8 10.1 - - - -
72B ARG* 3.2 44.6 - - + +
79B LEU* 3.7 6.7 - - + -
226B TES 5.7 2.0 - - - -
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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