Contacts of the strand formed by residues 37 - 42 (chain L) in PDB entry 6AL5
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 37 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4L LEU* 4.2 18.8 - - + -
23L CYS* 4.5 4.5 - - - -
29L VAL* 3.8 14.4 - - + -
35L SER 3.5 3.6 + - - -
36L TYR* 1.3 75.7 - - - +
38L ASN* 1.3 65.7 + - - +
39L TRP* 3.8 28.7 - - + +
52L ILE 4.4 0.5 - - - +
53L TYR 4.1 0.3 - - - -
54L ASP* 3.3 3.6 + - - +
55L ALA* 2.7 30.7 + - - +
75L PHE* 3.8 42.8 - - + -
92L CYS* 4.1 6.7 - - + -
93L GLN 3.4 29.4 - - - +
94L GLN* 4.1 10.8 - - + -
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Residues in contact with ASN 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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109H TYR 3.6 20.8 + - - +
110H ALA* 3.6 16.2 + - + +
36L TYR 4.9 2.4 + - - -
37L LEU* 1.3 76.2 - - - +
39L TRP* 1.3 65.5 + - - +
40L TYR* 4.2 5.8 - - + -
50L LEU* 4.2 0.7 - - + -
52L ILE 3.3 5.6 - - - +
53L TYR* 3.2 11.4 - - - +
54L ASP* 3.0 32.3 + - - +
91L TYR 4.5 0.2 - - - -
92L CYS* 3.1 8.8 - - - +
93L GLN* 2.7 66.1 + - - +
94L GLN* 4.8 2.0 - - - +
95L SER* 4.3 4.2 + - - +
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Residues in contact with TRP 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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6L GLN* 4.0 16.2 - - - -
21L ILE* 4.4 9.0 - - + -
22L THR 4.4 4.5 - - - -
23L CYS* 3.6 35.2 - - + -
37L LEU* 3.8 20.4 + - + +
38L ASN* 1.3 78.4 - - - +
40L TYR* 1.3 57.7 + - - +
50L LEU* 3.5 4.7 - - - +
51L LEU* 2.7 34.9 + - + -
52L ILE* 2.7 42.5 + - + +
55L ALA* 4.3 7.5 + - - +
67L SER 5.8 0.2 - - - -
68L GLY 6.1 0.2 - - - -
69L SER 5.2 0.2 + - - -
75L PHE* 4.4 1.8 - - - +
76L THR 3.9 31.9 + - - -
77L LEU* 3.5 44.2 - - + -
90L TYR* 4.9 6.3 - - + -
91L TYR 3.5 10.8 - - - -
92L CYS* 3.5 16.6 - - + -
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Residues in contact with TYR 40 (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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45H LEU* 5.8 0.2 - - + -
110H ALA* 3.4 2.8 - - - +
111H MET* 2.9 51.2 + - + +
114H TRP* 3.8 14.1 - + - -
38L ASN* 4.2 6.1 - - + -
39L TRP* 1.3 75.0 - - - +
41L GLN* 1.3 59.8 + - - +
42L GLN 4.1 0.2 + - - -
48L PRO* 4.1 23.1 - - + -
49L LYS 3.3 6.7 - - - +
50L LEU* 3.5 31.4 - - + -
51L LEU* 4.3 3.8 - - - -
89L THR 3.9 0.2 - - - +
90L TYR* 3.3 6.5 - - - +
91L TYR* 2.7 55.4 + - + +
93L GLN* 3.2 44.5 + - + -
102L PHE* 4.0 11.7 - + + -
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Residues in contact with GLN 41 (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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40L TYR* 1.3 73.6 - - - +
42L GLN* 1.3 63.0 + - - +
43L LYS* 4.1 18.0 + - - +
47L ALA 4.3 0.9 - - - +
48L PRO* 3.4 1.4 - - - +
49L LYS* 2.8 55.7 + - + +
51L LEU* 3.5 26.3 - - + +
66L PHE* 4.1 10.7 - - - -
85L GLU 4.3 3.2 + - - -
86L ASP* 4.0 17.4 + - - +
88L ALA* 3.9 16.0 - - + +
89L THR 3.5 3.6 - - - -
90L TYR* 2.8 34.6 + - + -
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Residues in contact with GLN 42 (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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39H GLN* 2.9 41.5 + - - +
45H LEU* 4.8 0.6 - - - +
95H TYR* 3.8 5.1 + - - -
40L TYR 4.1 0.4 + - - -
41L GLN* 1.3 73.7 - - - +
43L LYS* 1.3 63.2 - - - +
44L PRO* 4.1 2.6 - - - +
46L LYS 3.3 27.0 + - - +
47L ALA 4.6 0.4 - - - -
48L PRO* 3.7 31.0 - - + +
88L ALA* 4.0 3.5 - - - -
89L THR* 2.8 38.7 + - - -
91L TYR* 3.3 29.4 + - + -
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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