Contacts of the strand formed by residues 6 - 11 (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 GLN 6 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232H GLU* 4.3 7.6 - - - +
4L THR* 3.5 28.7 + - - +
5L PRO* 1.3 79.9 + - - +
7L ILE* 1.3 61.1 + - - +
26L TYR 3.7 0.9 - - - +
27L VAL* 3.2 6.4 - - - -
28L THR* 2.9 41.3 + - - +
29L GLN* 3.9 21.9 - - + +
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Residues in contact with ILE 7 (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* 4.3 6.1 - - + +
6L GLN* 1.3 82.5 + - - +
8L GLN* 1.3 73.8 + - - +
9L VAL* 4.2 10.3 - - + -
25L CYS* 3.8 28.3 - - - -
26L TYR 3.4 4.9 - - - +
27L VAL* 4.5 7.2 - - + -
80L CYS* 4.6 3.1 - - + +
82L VAL* 3.2 41.5 - - + -
91L LYS* 4.2 16.6 - - + +
93L VAL* 3.8 35.1 - - + +
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Residues in contact with GLN 8 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231H VAL* 3.4 27.5 - - + +
232H GLU* 3.4 32.1 + - - +
234H ARG* 2.7 42.2 + - - +
7L ILE* 1.3 80.2 - - - +
9L VAL* 1.3 64.3 + - - +
10L TYR* 3.7 13.9 - - + -
25L CYS* 3.4 3.3 - - - -
26L TYR* 3.0 40.5 + - + +
93L VAL* 5.6 0.7 - - - -
99L MET 4.5 1.1 - - - +
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Residues in contact with VAL 9 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234H ARG* 5.1 0.2 + - - -
7L ILE* 4.2 3.4 - - + -
8L GLN* 1.3 75.7 - - - +
10L TYR* 1.3 66.6 + - - +
23L LEU* 3.8 12.6 - - + -
24L ASN 3.3 10.5 - - - +
25L CYS* 4.4 2.2 - - + -
39L MET* 5.5 1.1 - - + -
78L TYR 5.1 1.3 - - - +
79L ALA 5.2 1.6 - - - -
80L CYS* 3.7 24.5 - - + +
93L VAL* 3.4 36.3 - - + +
94L TYR 4.2 2.9 - - - +
95L TRP* 3.5 46.6 - - + +
96L ASP 4.7 3.5 + - - +
99L MET* 4.5 9.0 - - - +
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Residues in contact with TYR 10 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234H ARG* 3.2 55.6 - - + +
235H PRO* 2.5 35.4 + - - +
242H GLN* 3.4 23.3 - - - -
8L GLN* 3.7 19.5 - - + -
9L VAL* 1.3 80.7 - - - +
11L SER* 1.3 60.4 + - - +
23L LEU* 3.2 5.9 - - - +
24L ASN* 2.5 63.4 + - + +
26L TYR* 3.6 24.7 - - + +
65L LEU* 4.0 3.8 - - - +
95L TRP* 3.7 9.9 - - - +
99L MET* 4.5 2.0 - - - +
901L GOL 3.6 4.7 - - - +
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Residues in contact with SER 11 (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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242H GLN* 3.2 8.5 + - - -
10L TYR* 1.3 81.9 - - - +
12L ARG* 1.3 67.6 + - - +
13L HIS 2.9 23.0 + - - -
15L PRO* 3.9 7.3 - - - +
21L ASN* 3.8 11.4 + - - -
22L ILE 3.0 13.5 - - - -
24L ASN* 4.3 0.4 - - - -
70L PHE* 4.0 15.5 - - - -
95L TRP* 4.2 4.7 + - - +
901L GOL 2.9 30.3 + - - -
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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