Contacts of the strand formed by residues 17 - 23 (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 SER 17 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11M SER 5.1 1.2 - - - +
12M GLY* 4.4 9.6 - - - -
16M GLN* 1.3 91.3 + - - +
18M VAL* 1.3 66.8 + - - +
19M THR 4.4 0.3 + - - -
76M THR* 5.5 5.3 - - - -
77M VAL 2.7 7.6 - - - -
78M SER* 2.7 35.3 + - - -
80M LEU* 5.3 0.4 - - - +
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Residues in contact with VAL 18 (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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10M ALA* 5.4 2.2 - - + +
17M SER* 1.3 78.9 - - - +
19M THR* 1.3 57.3 + - - +
20M ILE* 3.5 13.7 - - + -
76M THR* 2.7 21.0 - - - -
77M VAL* 2.6 61.7 + - + +
80M LEU* 4.9 13.2 - - + -
105M THR* 4.7 0.2 - - + -
106M LYS* 3.2 52.3 - - + +
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Residues in contact with THR 19 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10M ALA* 4.2 5.5 - - - +
17M SER 4.3 0.4 + - - -
18M VAL* 1.3 72.1 - - - +
20M ILE* 1.3 57.6 + - - +
21M SER 4.3 0.4 + - - -
74M SER* 5.3 7.0 - - - +
75M LEU 3.4 4.3 - - - -
76M THR* 3.4 20.9 - - + -
105M THR* 2.8 22.9 - - - +
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Residues in contact with ILE 20 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18M VAL* 3.5 9.4 - - + -
19M THR* 1.3 78.1 - - - +
21M SER* 1.3 57.5 + - - +
37M TRP* 2.8 40.7 - - + -
49M ILE* 5.6 0.4 - - + -
74M SER* 2.9 31.0 - - - -
75M LEU* 2.7 45.1 + - + +
77M VAL* 3.8 2.9 - - + -
88M TYR* 4.0 8.5 - - + -
105M THR* 2.6 59.5 - - + +
106M LYS* 3.1 22.0 - - + -
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Residues in contact with SER 21 (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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5M THR 3.3 2.9 + - - -
6M GLN* 2.6 40.4 + - - +
7M PRO* 2.5 41.1 - - - +
19M THR 4.3 0.4 - - - -
20M ILE* 1.3 73.7 - - - +
22M CYS* 1.3 58.9 + - - +
23M THR* 4.2 2.5 + - - -
37M TRP* 3.4 1.7 - - - -
73M ALA 3.5 2.9 - - - -
74M SER* 4.5 4.5 - - - -
105M THR* 4.0 4.8 + - - +
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Residues in contact with CYS 22 (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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4M LEU* 2.9 34.1 - - - -
5M THR 2.8 8.1 - - - -
6M GLN* 3.4 11.0 - - - -
21M SER* 1.3 75.0 + - - +
23M THR* 1.3 63.7 - - - +
29M VAL* 3.7 10.4 - - + +
72M THR* 3.6 2.0 - - - +
73M ALA* 2.8 34.9 + - - +
90M CYS* 2.3 54.7 - - - -
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Residues in contact with THR 23 (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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4M LEU* 2.9 18.2 - - - +
5M THR* 2.7 43.8 + - - +
21M SER* 4.2 1.8 + - - -
22M CYS* 1.3 76.0 - - - +
24M GLY* 1.3 69.9 - - - +
71M ASN* 4.9 2.0 - - + -
72M THR* 3.1 41.5 - - + +
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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