Contacts of the strand formed by residues 71 - 80 (chain B) in PDB entry 1MCH
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 71 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4B LEU* 5.6 0.3 - - - +
22B CYS 3.5 2.9 - - - +
23B THR* 3.5 24.1 - - + +
24B GLY* 3.1 39.3 + - - +
25B THR 6.4 0.2 - - - -
29B VAL* 4.4 18.5 + - - +
30B GLY* 5.5 2.6 - - - -
69B SER* 4.8 0.2 - - - -
70B GLY* 1.3 75.9 - - - +
72B THR* 1.3 63.2 + - - +
73B ALA 4.2 0.2 + - - -
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Residues in contact with THR 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B SER* 3.6 32.3 - - - +
22B CYS 3.4 12.1 - - - +
23B THR* 3.2 25.7 + - - +
67B SER 3.8 0.2 - - - +
68B LYS* 3.7 2.1 - - - -
69B SER* 3.0 38.8 + - - -
70B GLY 3.9 2.8 + - - +
71B ASN* 1.3 80.0 - - - +
73B ALA* 1.3 67.7 + - - +
74B SER* 4.2 2.6 + - - +
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Residues in contact with ALA 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B CYS* 2.8 36.6 + - - +
35B VAL* 3.9 34.1 - - + -
37B TRP* 3.5 11.2 - - - +
53B VAL* 5.8 6.1 - - + +
67B SER 3.0 11.9 - - - +
68B LYS* 5.5 0.2 - - - -
71B ASN 4.2 0.2 + - - -
72B THR* 1.3 75.5 - - - +
74B SER* 1.3 63.5 + - - +
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Residues in contact with SER 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B THR* 3.4 14.3 + - - +
20B ILE 3.3 6.3 - - - -
21B SER* 3.4 19.9 + - - +
37B TRP* 3.6 7.9 + - - -
65B SER 5.1 0.2 - - - -
66B GLY* 3.2 19.1 - - - -
67B SER* 3.1 27.4 + - - -
72B THR* 4.0 4.3 + - - +
73B ALA* 1.3 76.2 - - - +
75B LEU* 1.3 64.6 + - - +
76B THR* 5.0 2.5 - - - -
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B THR* 3.6 3.7 + - - -
20B ILE* 2.8 59.4 + - + +
37B TRP* 3.8 30.3 - - + +
49B ILE* 3.8 11.9 - - + -
50B ILE* 4.4 6.5 - - + -
64B PHE* 3.9 17.0 - - + -
65B SER* 3.4 28.5 - - - +
66B GLY* 4.5 0.9 - - - +
74B SER* 1.3 79.2 - - - +
76B THR* 1.3 56.2 + - - +
77B VAL* 3.3 6.6 + - + -
88B TYR* 3.8 28.5 - - + -
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Residues in contact with THR 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B SER* 5.5 5.2 - - - -
18B VAL 3.4 6.5 - - - +
19B THR* 3.5 27.1 + - - +
63B ARG 3.5 3.3 - - - +
65B SER* 2.9 46.9 + - - -
67B SER* 4.9 4.0 + - - -
74B SER* 5.1 1.9 - - - -
75B LEU* 1.3 69.0 + - - +
77B VAL* 1.3 64.7 + - - +
78B SER* 3.4 9.3 + - - -
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Residues in contact with VAL 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B SER* 3.2 6.4 - - - -
18B VAL* 2.8 43.9 + - + +
20B ILE* 4.1 21.1 - - + -
63B ARG* 3.7 12.1 - - - +
64B PHE* 3.6 31.6 - - + +
75B LEU* 4.1 4.7 - - + +
76B THR* 1.3 70.9 - - - +
78B SER* 1.3 61.5 - - - +
79B GLY 4.0 0.4 - - - -
80B LEU* 4.1 21.8 - - + -
84B ASP* 3.9 26.2 - - + +
88B TYR* 4.4 6.7 - - + +
107B VAL* 5.7 0.9 - - + -
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Residues in contact with SER 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B SER* 3.8 14.8 + - - -
62B ASP 6.1 0.2 - - - -
63B ARG* 2.9 40.1 + - - +
76B THR* 3.4 6.5 + - - -
77B VAL* 1.3 73.4 - - - +
79B GLY* 1.3 58.2 + - - +
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Residues in contact with GLY 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B GLY* 3.7 20.2 + - - -
17B SER* 4.1 2.8 + - - -
63B ARG* 4.6 5.2 - - - -
77B VAL 4.0 0.6 + - - -
78B SER* 1.3 74.2 + - - +
80B LEU* 1.3 61.2 + - - +
81B GLN* 2.8 30.7 + - - +
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Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B GLY* 3.4 36.6 - - - +
13B SER 3.8 1.6 - - - +
14B LEU* 3.4 8.4 - - - +
15B GLY* 3.0 29.5 + - - +
16B GLN 3.5 26.0 + - - +
18B VAL* 3.9 24.0 - - + +
77B VAL* 4.1 13.5 - - + +
78B SER* 3.9 0.4 - - - +
79B GLY* 1.3 80.9 - - - +
81B GLN* 1.3 77.6 + - - +
84B ASP* 3.8 24.2 - - + -
107B VAL* 4.9 10.5 - - + -
108B THR 4.5 3.8 - - - +
109B VAL* 4.7 7.0 - - + -
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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