Contacts of the strand formed by residues 31 - 37 (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 ASN 31 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C SER* 2.5 31.0 + - - -
29D HIS* 4.0 2.6 - - - +
30D ASN* 1.3 90.7 + - - +
32D MET* 1.3 64.8 + - - +
33D TYR* 2.9 25.6 - - + +
49D SER 3.4 13.1 + - - -
50D TYR* 3.6 15.8 + - - +
94D SER* 3.0 23.4 - - - -
95D GLY 3.0 22.4 + - - +
96D GLY* 4.1 2.7 - - - -
97D GLY 3.8 9.9 + - - -
6Q TYR* 4.9 4.4 - - - -
7Q SER* 5.5 0.6 + - - -
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Residues in contact with MET 32 (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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23D CYS* 3.4 33.7 - - - +
24D ASN 3.9 9.9 - - - +
25D GLN* 2.8 29.2 - - - +
29D HIS 5.0 0.2 - - - +
30D ASN 4.1 0.8 + - - -
31D ASN* 1.3 82.9 - - - +
33D TYR* 1.3 67.9 + - - +
48D TYR* 3.3 1.2 - - - -
49D SER 3.0 28.8 + - - +
69D ARG* 4.1 14.5 - - - +
74D ASN 3.3 9.4 - - - +
75D PHE* 3.2 52.4 - - + -
93D ALA 2.8 13.7 - - - +
94D SER* 4.1 8.1 - - - +
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Residues in contact with TYR 33 (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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101C ALA* 6.3 0.2 - - + -
102C SER* 2.7 44.7 + - - -
103C ALA* 3.5 30.5 - - + -
31D ASN* 2.9 22.1 - - + +
32D MET* 1.3 88.6 - - - +
34D TRP* 1.3 60.5 + - - +
35D TYR* 3.5 12.3 - + + -
45D LEU* 3.4 15.0 - - + -
47D HIS 3.5 6.3 - - - -
48D TYR* 3.0 29.4 - + + -
49D SER 4.6 3.8 - - - -
50D TYR* 6.4 0.4 - + - -
75D PHE* 3.7 4.8 - - - -
92D CYS* 2.8 10.4 - - - +
93D ALA* 2.6 47.7 + - + -
94D SER 4.5 8.5 - - - -
95D GLY* 5.4 0.7 - - - -
106D LEU* 5.6 2.0 - - + -
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Residues in contact with TRP 34 (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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6D GLN* 4.2 10.3 - - - -
21D LEU* 3.8 32.5 - - + -
23D CYS* 3.4 22.4 - - + -
33D TYR* 1.3 73.2 - - - +
35D TYR* 1.3 58.4 + - - +
45D LEU* 3.2 5.9 - - - +
46D ILE* 2.3 53.3 + - + -
47D HIS 3.0 10.3 + - - +
67D ALA* 4.9 3.8 - - + -
75D PHE* 3.7 33.0 + + - -
76D SER 4.0 1.5 - - - -
77D LEU* 3.3 42.9 - - + +
90D TYR* 4.1 15.3 - - + -
91D PHE* 3.1 34.5 - - - -
92D CYS* 3.3 32.5 - - + -
112D THR* 5.1 2.5 - - - -
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Residues in contact with TYR 35 (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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103C ALA* 4.0 5.4 - - - +
104C LEU* 2.7 43.4 + - - +
105C THR* 5.3 1.3 - - - -
106C PHE* 4.2 8.2 - + - -
33D TYR* 3.5 25.6 - - + +
34D TRP* 1.3 78.0 - - - +
36D ARG* 1.3 61.1 + - - +
37D GLN 3.9 0.2 - - - -
43D LEU* 3.1 45.1 - - + -
44D ARG* 2.7 26.7 - - - -
45D LEU* 3.2 24.7 - - + +
46D ILE* 3.7 4.5 - - - +
90D TYR* 3.0 30.3 - - - +
91D PHE* 2.5 22.6 + - + +
93D ALA* 4.1 13.9 - - + -
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Residues in contact with ARG 36 (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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35D TYR* 1.3 75.0 - - - +
37D GLN* 1.3 59.3 + - - +
42D GLY 3.0 0.5 - - - +
44D ARG* 2.5 59.9 + - - +
46D ILE* 3.7 10.5 - - + -
60D ILE* 4.4 18.0 - - + +
65D TYR* 2.9 33.2 + - - -
85D SER* 2.7 36.7 + - - +
87D THR 4.8 4.0 + - - -
88D SER* 3.2 22.7 - - - +
89D VAL 3.3 6.5 - - - -
90D TYR* 3.3 16.4 - - + -
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Residues in contact with GLN 37 (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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89C PHE* 3.6 26.7 - - + -
108C SER 5.1 0.2 - - - +
36D ARG* 1.3 70.8 - - - +
38D ASP* 1.3 100.1 + - - +
42D GLY* 2.8 7.4 - - - -
43D LEU* 3.1 43.4 - - + +
88D SER* 3.3 0.3 + - - -
89D VAL* 2.9 27.4 + - + +
91D PHE* 5.1 8.0 - - + -
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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