Contacts of the strand formed by residues 46 - 51 (chain L) 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 GLU 46 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98K PHE* 4.2 3.1 - - - -
37L VAL* 3.7 0.4 - - - +
38L ARG* 2.9 79.3 + - + +
44L GLY 5.4 0.9 - - - +
45L LEU* 1.3 75.3 - - - +
47L TRP* 1.3 74.7 + - - +
48L VAL* 3.8 2.4 + - + +
63L SER* 4.8 11.8 + - - -
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Residues in contact with TRP 47 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94K TRP* 3.4 32.5 - + - -
95K PRO* 3.6 23.3 - - + -
96K LEU* 3.6 60.1 + - + +
98K PHE* 3.9 16.0 - - + -
35L PHE* 3.8 14.7 - + - -
36L TRP 4.2 4.0 - - - -
37L VAL* 4.4 5.2 - - + -
46L GLU* 1.3 84.2 - - - +
48L VAL* 1.3 69.4 + - - +
49L SER* 3.2 36.8 + - - +
50L TRP* 4.5 3.8 - - + +
59L LYS* 4.4 3.6 - - + -
60L TYR* 4.1 4.5 - - - -
61L ALA* 3.1 40.7 - - - +
106L PHE* 4.4 6.1 - + + -
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Residues in contact with VAL 48 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36L TRP* 3.4 20.7 + - + +
37L VAL 5.2 0.2 - - - -
38L ARG* 3.6 39.7 - - + +
46L GLU* 3.8 7.2 - - + +
47L TRP* 1.3 91.0 - - - +
49L SER* 1.3 72.2 + - - +
60L TYR* 3.3 3.8 - - - +
61L ALA* 3.0 31.5 + - + +
63L SER* 6.1 0.4 - - - +
64L VAL* 3.9 25.3 - - + +
68L PHE* 4.7 11.7 - - + -
81L LEU* 4.7 4.5 - - + -
94L TYR* 4.9 4.7 - - + -
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Residues in contact with SER 49 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35L PHE* 3.3 5.4 - - - -
36L TRP* 3.2 32.1 + - - -
47L TRP* 3.2 16.2 + - - +
48L VAL* 1.3 90.7 - - - +
50L TRP* 1.3 61.7 + - - +
60L TYR* 3.0 26.2 - - - +
70L ILE* 3.5 29.0 - - - +
81L LEU* 4.3 7.5 - - - +
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Residues in contact with TRP 50 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33L PRO* 3.7 13.4 - - + +
34L MET 3.2 13.9 - - - -
35L PHE* 3.3 33.8 - + + -
47L TRP* 4.5 5.6 - - + +
49L SER* 1.3 78.1 + - - +
51L ILE* 1.3 73.0 + - - +
52L GLY* 3.9 14.1 - - - -
53L PRO* 5.3 1.1 - - + -
57L ILE* 3.8 45.3 - - + -
58L THR* 3.4 27.7 - - - -
59L LYS* 3.4 43.4 + - + -
60L TYR 4.1 4.2 - - - +
70L ILE* 3.8 6.6 - - - +
99L GLU* 3.3 20.5 + - - -
104L TRP* 5.6 11.1 - + - -
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Residues in contact with ILE 51 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33L PRO* 3.4 1.7 - - - +
34L MET 2.8 31.6 + - - +
50L TRP* 1.3 87.1 - - - +
52L GLY* 1.3 72.3 + - - +
55L GLY* 3.7 24.5 - - - +
57L ILE 3.8 2.5 - - - -
58L THR* 4.0 14.1 - - + -
70L ILE* 3.6 34.8 - - + +
71L SER* 4.3 14.6 - - - +
72L ARG* 2.9 38.4 - - + +
79L LEU* 4.5 5.2 - - + -
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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