Contacts of the strand formed by residues 72 - 78 (chain M) in PDB entry 1MCW
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 THR 72 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22M CYS 3.6 2.7 - - - +
23M THR* 3.1 39.7 - - + +
68M LYS* 2.6 24.6 - - - +
69M SER 3.0 12.5 + - - -
70M GLY 3.2 2.7 + - - -
71M ASN* 1.3 88.0 + - - +
73M ALA* 1.3 58.2 + - - +
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Residues in contact with ALA 73 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20M ILE 3.8 0.2 - - - +
21M SER 3.5 0.5 - - - -
22M CYS* 2.8 43.2 + - + +
29M VAL* 3.2 16.6 - - + -
35M VAL* 5.5 4.5 - - + -
37M TRP* 4.1 3.2 - - - +
67M SER 3.9 1.3 - - - +
68M LYS* 2.7 44.9 - - + +
72M THR* 1.3 72.7 - - - +
74M SER* 1.3 61.3 + - - +
90M CYS* 5.8 1.1 - - - -
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Residues in contact with SER 74 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19M THR* 5.3 6.9 - - - +
20M ILE 2.9 21.3 - - - -
21M SER* 4.5 3.4 - - - -
37M TRP* 4.4 5.6 + - - -
66M GLY* 3.4 1.3 - - - -
67M SER* 2.3 48.7 + - - +
68M LYS* 5.2 1.6 - - - -
73M ALA* 1.3 75.9 - - - +
75M LEU* 1.3 65.9 + - - +
76M THR* 6.3 0.4 - - - -
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Residues in contact with LEU 75 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19M THR* 4.2 0.4 - - - -
20M ILE* 2.7 61.0 + - + +
37M TRP* 2.9 39.5 - - + +
49M ILE* 4.7 5.4 - - + -
50M ILE* 2.8 36.6 - - + -
64M PHE* 5.1 0.4 - - + -
65M SER 2.5 24.9 - - - +
66M GLY* 4.1 0.7 - - - -
74M SER* 1.3 79.2 - - - +
76M THR* 1.3 60.4 + - - +
77M VAL* 4.0 9.9 - - + -
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Residues in contact with THR 76 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17M SER* 5.5 4.9 - - - -
18M VAL 2.7 18.4 - - - +
19M THR* 3.4 26.7 - - + -
64M PHE* 3.0 2.6 - - - -
65M SER* 2.3 60.3 + - - -
74M SER* 6.3 0.4 - - - -
75M LEU* 1.3 70.3 - - - +
77M VAL* 1.3 64.2 + - - +
78M SER* 4.1 1.7 + - - -
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Residues in contact with VAL 77 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17M SER* 2.7 15.0 - - - -
18M VAL* 2.6 63.9 + - + +
20M ILE* 3.8 15.7 - - + -
63M ARG* 2.8 14.6 - - - +
64M PHE* 3.0 39.3 - - + -
75M LEU* 4.0 3.4 - - + -
76M THR* 1.3 77.9 - - - +
78M SER* 1.3 56.4 + - - +
79M GLY 3.3 2.1 + - - +
84M ASP* 4.4 0.9 - - - +
106M LYS* 3.1 24.5 - - + +
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Residues in contact with SER 78 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16M GLN 4.3 1.4 + - - -
17M SER* 2.7 14.7 + - - -
63M ARG* 2.8 42.6 + - - +
65M SER* 5.2 0.6 + - - -
76M THR* 4.1 2.9 + - - -
77M VAL* 1.3 67.7 - - - +
79M GLY* 1.3 70.8 + - - +
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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