Contacts of the strand formed by residues 88 - 95 (chain D) 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 SER 88 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36D ARG* 3.2 39.9 - - - +
37D GLN 3.3 3.3 + - - -
38D ASP* 3.2 28.1 - - - +
44D ARG* 4.9 0.2 - - - -
86D GLN 3.3 5.3 + - - -
87D THR* 1.3 78.7 - - - +
89D VAL* 1.3 77.0 + - - +
90D TYR* 4.2 7.9 - - - -
113D ARG* 3.7 1.7 - - - +
114D LEU 3.2 26.7 + - - +
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Residues in contact with VAL 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D ARG 3.3 2.1 - - - -
37D GLN* 2.9 42.4 + - - +
38D ASP* 3.4 12.6 - - - +
88D SER* 1.3 87.4 + - - +
90D TYR* 1.3 60.4 + - - +
91D PHE* 3.6 22.2 - - + -
112D THR 3.1 21.1 - - - +
113D ARG* 3.8 20.9 - - + +
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Residues in contact with TYR 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D LEU* 4.2 20.6 - - + -
34D TRP* 4.1 15.6 - - + -
35D TYR 3.0 20.9 - - - +
36D ARG* 3.3 35.7 - - + -
46D ILE* 4.8 3.8 - - + -
65D TYR* 3.2 35.5 + + - -
77D LEU* 6.3 2.7 - - + -
79D LEU* 4.9 3.4 - - + -
86D GLN* 2.7 25.8 + - - -
88D SER* 4.2 5.8 - - - -
89D VAL* 1.3 72.3 - - - +
91D PHE* 1.3 68.5 - - - +
112D THR* 2.6 39.0 + - - +
113D ARG* 4.2 1.8 - - - +
114D LEU* 3.5 40.5 - - + +
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Residues in contact with PHE 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C GLN* 4.1 27.1 - - + -
42C GLY* 6.0 0.7 - - - -
43C LEU* 5.4 10.1 - - + -
34D TRP* 3.1 7.6 - - - -
35D TYR* 2.5 42.6 + - + +
37D GLN* 5.1 5.8 - - + -
43D LEU* 4.3 22.0 - - + +
89D VAL* 3.6 28.3 - - + -
90D TYR* 1.3 91.7 - - - +
92D CYS* 1.3 60.3 + - - +
108D PHE* 4.9 15.0 - + + -
110D ALA* 4.4 6.1 - - - -
111D GLY* 4.0 27.1 - - - -
112D THR 4.2 2.7 - - - -
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Residues in contact with CYS 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D VAL* 3.5 16.1 - - - +
6D GLN* 3.8 14.0 - - - +
23D CYS* 2.0 48.7 - - - -
33D TYR 2.8 13.0 - - - +
34D TRP* 3.3 24.0 - - + +
35D TYR* 5.4 0.4 - - - -
75D PHE* 4.9 1.8 - - + -
91D PHE* 1.3 73.9 - - - +
93D ALA* 1.3 59.7 + - - +
108D PHE* 3.5 18.9 - - - -
110D ALA 4.4 5.6 + - - +
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Residues in contact with ALA 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D VAL* 5.5 0.2 - - - -
32D MET* 2.8 31.9 - - - +
33D TYR* 2.6 36.7 + - + -
35D TYR* 4.1 13.0 - - + +
91D PHE 4.3 0.4 + - - -
92D CYS* 1.3 75.0 - - - +
94D SER* 1.3 66.0 + - - +
106D LEU* 4.6 6.1 - - + -
108D PHE* 3.5 21.5 - - + -
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Residues in contact with SER 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D VAL* 3.4 20.9 - - - +
25D GLN* 4.6 1.6 + - - +
27D ASN* 3.7 25.0 + - - -
29D HIS* 4.0 5.2 - - - -
31D ASN 3.0 14.1 - - - -
32D MET* 4.1 12.1 - - - +
33D TYR* 4.5 3.3 - - - -
93D ALA* 1.3 77.5 + - - +
95D GLY* 1.3 58.4 + - - +
106D LEU* 2.8 30.4 - - - +
107D TYR 3.8 10.3 - - - -
108D PHE* 4.0 5.1 - - - -
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Residues in contact with GLY 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D HIS* 3.2 20.3 - - - +
30D ASN 3.7 1.2 + - - -
31D ASN* 3.0 34.4 + - - +
33D TYR* 5.4 0.2 - - - -
94D SER* 1.3 79.6 - - - +
96D GLY* 1.3 58.6 + - - -
97D GLY 4.0 0.2 - - - -
105D THR 3.5 17.5 - - - -
106D LEU* 3.8 7.2 - - - -
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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