Contacts of the strand formed by residues 21 - 30 (chain L) in PDB entry 1MWA
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 ASN 21 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11L SER* 3.9 5.2 + - - -
12L ARG 3.7 2.3 + - - -
13L HIS* 2.8 61.2 + - - +
14L PRO 3.8 9.7 + - - -
15L PRO* 3.9 10.7 - - - +
16L GLU 4.6 2.4 - - - +
19L LYS 4.2 4.7 - - - +
20L PRO* 1.3 76.7 + - - +
22L ILE* 1.3 75.4 + - - +
69L GLU* 3.4 5.0 - - - +
70L PHE* 2.5 60.4 + - + +
72L PRO* 4.4 3.1 - - + +
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Residues in contact with ILE 22 (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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11L SER* 3.0 7.6 - - - -
12L ARG* 2.9 73.2 + - + +
13L HIS* 5.4 3.8 - - + +
21L ASN* 1.3 89.4 + - - +
23L LEU* 1.3 61.9 + - - +
24L ASN* 3.8 8.1 - - - +
67L HIS* 3.7 35.9 - - + +
68L THR 3.3 8.5 - - - +
69L GLU* 4.0 20.6 - - + +
70L PHE* 3.5 2.7 - - - -
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Residues in contact with LEU 23 (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 VAL* 3.8 23.3 - - + -
10L TYR 3.2 24.5 - - - +
22L ILE* 1.3 69.9 - - - +
24L ASN* 1.3 65.0 + - - +
39L MET* 3.3 17.7 - - + +
46L ILE* 5.5 0.9 - - + -
67L HIS* 3.1 5.2 - - - -
68L THR* 2.7 43.6 + - - +
70L PHE* 3.5 27.3 - - + -
78L TYR* 3.1 47.8 - - + -
79L ALA 5.2 2.0 - - - +
95L TRP* 3.9 11.7 - - + +
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Residues in contact with ASN 24 (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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235H PRO 3.6 1.1 + - - -
236H ALA 2.5 32.5 + - - +
8L GLN 4.3 0.4 - - - -
9L VAL* 3.3 9.7 - - - +
10L TYR* 2.5 72.0 + - + +
12L ARG* 4.0 10.6 + - - +
22L ILE* 3.8 7.4 - - - +
23L LEU* 1.3 74.2 - - - +
25L CYS* 1.3 61.7 + - - +
26L TYR 4.0 0.4 - - - -
39L MET* 4.2 1.3 - - - +
65L LEU* 4.3 12.0 - - + +
66L ALA 3.5 2.3 - - - +
67L HIS* 3.0 25.5 - - - +
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Residues in contact with CYS 25 (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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7L ILE* 3.8 18.8 - - - -
8L GLN 3.4 4.0 - - - -
9L VAL* 4.4 1.6 - - + -
24L ASN* 1.3 74.4 - - - +
26L TYR* 1.3 58.6 + - - +
27L VAL* 3.8 14.5 + - - +
37L ILE* 4.3 1.8 - - - -
39L MET* 4.0 13.2 - - + -
64L ILE 4.0 0.9 - - - +
65L LEU* 4.2 0.7 - - - -
66L ALA* 2.7 35.9 + - + +
80L CYS* 2.0 53.4 - - + -
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Residues in contact with TYR 26 (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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232H GLU* 4.8 7.8 + - - -
233H THR 4.0 13.8 + - - -
234H ARG* 3.8 10.1 - - + -
235H PRO* 3.5 40.6 - - + +
6L GLN 3.7 0.7 - - - +
7L ILE* 3.4 4.0 - - - -
8L GLN* 3.0 42.2 + - + +
10L TYR* 3.6 21.1 - - + +
24L ASN 4.0 0.2 - - - -
25L CYS* 1.3 72.3 - - - +
27L VAL* 1.3 59.4 - - - +
28L THR* 3.5 29.0 - - + +
63L TYR* 4.1 27.8 - + + -
64L ILE 3.7 17.3 - - - -
65L LEU* 3.9 9.2 - - + -
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Residues in contact with VAL 27 (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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5L PRO* 3.6 28.0 - - + -
6L GLN 3.2 6.1 - - - +
7L ILE* 4.5 8.1 - - + -
25L CYS* 4.0 21.5 - - - +
26L TYR* 1.3 75.9 - - - +
28L THR* 1.3 66.5 + - - +
30L PHE* 3.5 15.3 - - + -
35L ILE* 4.1 9.4 - - + -
37L ILE* 3.6 29.2 - - + -
63L TYR* 3.3 3.5 - - - -
64L ILE 3.1 30.9 + - - +
82L VAL* 4.2 10.8 - - + -
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Residues in contact with THR 28 (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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232H GLU* 3.0 26.0 + - - +
5L PRO* 3.1 5.4 - - - +
6L GLN* 2.9 33.6 + - - +
26L TYR* 3.5 42.8 - - + +
27L VAL* 1.3 79.8 - - - +
29L GLN* 1.3 80.3 + - - +
30L PHE* 3.0 6.2 + - - -
62L PHE 3.8 7.4 - - - -
63L TYR* 3.9 10.3 - - + -
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Residues in contact with GLN 29 (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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232H GLU* 3.5 25.3 - - - +
3L LYS* 3.0 19.4 - - + +
4L THR 2.9 20.6 - - - +
6L GLN* 3.9 16.6 - - + +
28L THR* 1.3 87.1 - - - +
30L PHE* 1.3 57.9 + - - +
57L SER* 5.5 2.1 + - - -
59L ASP* 3.4 15.6 + - - -
61L SER* 3.0 33.2 + - - -
62L PHE 3.5 5.1 + - - -
63L TYR* 5.2 0.2 - - - +
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Residues in contact with PHE 30 (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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3L LYS* 3.5 10.8 - - - +
5L PRO* 3.6 19.1 - - + -
27L VAL* 3.5 36.3 - - + -
28L THR 3.0 10.7 + - - -
29L GLN* 1.3 78.8 - - - +
31L HIS* 1.3 62.1 + - - +
32L PRO 3.4 12.8 - - - -
33L PRO 3.5 22.4 - - - -
35L ILE* 3.7 24.9 - - + -
54L MET* 4.3 4.3 - - - -
61L SER* 3.8 1.0 - - - -
62L PHE* 2.9 53.5 + - + -
64L ILE* 3.6 24.9 - - + -
84L HIS* 3.9 6.3 - - + +
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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