Contacts of the strand formed by residues 34 - 39 (chain L) in PDB entry 6CMO
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 VAL 34 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116H TYR* 4.7 2.9 - - - +
30L VAL* 5.5 3.8 - - + -
31L SER 4.9 1.8 - - - +
32L SER 3.9 2.2 + - - -
33L ALA* 1.3 81.6 - - - +
35L ALA* 1.3 64.3 + - - +
36L TRP* 3.9 25.8 - - + +
50L TYR 3.9 0.2 - - - -
51L SER* 3.2 11.3 + - - +
52L ALA* 3.0 41.6 + - + -
72L PHE* 3.6 41.1 - - + -
89L CYS* 4.8 8.3 - - - -
90L GLN* 3.3 15.5 - - - +
91L GLN* 5.2 2.5 - - + -
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Residues in contact with ALA 35 (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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116H TYR 3.9 14.4 - - - +
34L VAL* 1.3 77.6 - - - +
36L TRP* 1.3 67.2 + - - +
37L TYR* 3.9 19.5 - - + +
47L LEU* 3.9 7.6 - - + -
49L ILE 3.3 14.6 - - - +
88L TYR 3.6 2.3 - - - +
89L CYS* 4.0 0.3 - - - -
90L GLN* 3.2 46.7 + - - +
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Residues in contact with TRP 36 (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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9L PRO* 6.0 2.0 - - + -
22L ILE* 3.9 35.0 - - + -
24L CYS* 3.6 34.8 - - + -
34L VAL* 3.9 17.6 - - + +
35L ALA* 1.3 78.7 - - - +
37L TYR* 1.3 64.4 + - - +
47L LEU* 4.2 0.5 - - - +
48L LEU* 3.2 36.8 + - + +
49L ILE* 3.4 26.4 + - + +
52L ALA* 5.4 4.6 + - - +
72L PHE* 4.6 15.4 - - + +
73L THR 5.7 1.4 + - - -
74L LEU* 4.4 40.4 - - + +
87L TYR* 4.5 11.0 - - + -
88L TYR 3.4 23.3 - - - -
89L CYS* 3.8 18.2 - - + -
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Residues in contact with TYR 37 (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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117H GLY* 3.6 7.6 - - - -
118H MET* 2.8 47.8 + - + +
121H TRP* 4.0 15.0 - + - -
35L ALA* 3.9 12.4 - - + +
36L TRP* 1.3 73.9 - - - +
38L GLN* 1.3 61.2 + - - +
39L GLN* 5.6 0.4 - - + -
45L PRO* 4.3 16.8 - - + -
46L LYS 3.3 19.7 - - - +
47L LEU* 3.6 26.0 - - + -
48L LEU* 4.6 1.1 - - - -
86L THR 3.7 0.3 - - - +
87L TYR* 3.3 10.7 - - - -
88L TYR* 3.0 46.1 + + + +
90L GLN* 3.8 36.1 + - + -
99L PHE* 5.5 3.8 - + - -
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Residues in contact with GLN 38 (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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37L TYR* 1.3 73.2 - - - +
39L GLN* 1.3 60.9 + - - +
40L LYS* 4.1 9.5 - - - +
43L LYS* 4.4 17.1 - - + +
44L ALA 4.0 2.6 - - - +
45L PRO* 3.6 6.8 - - - +
46L LYS* 3.3 51.9 + - + +
48L LEU* 4.1 18.6 - - + +
63L PHE* 5.3 4.5 - - - -
83L ASP* 5.1 7.3 - - - +
85L ALA* 5.0 7.0 - - + +
86L THR 3.5 5.2 - - - +
87L TYR* 3.6 30.4 + - + -
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Residues in contact with GLN 39 (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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48H LEU* 5.6 4.5 - - + -
98H TYR* 4.5 11.1 + - - -
37L TYR* 4.1 0.6 + - + -
38L GLN* 1.3 73.4 - - - +
40L LYS* 1.3 77.0 + - - +
41L PRO* 4.3 5.1 - - + +
42L GLY 4.8 0.4 - - - +
43L LYS 2.4 27.4 + - - +
44L ALA 3.4 1.0 - - - -
45L PRO* 3.2 38.8 - - + +
85L ALA* 3.7 3.3 - - - -
86L THR* 2.8 53.3 + - - +
88L TYR* 4.4 24.2 - - + +
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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