Contacts of the strand formed by residues 35 - 40 (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 VAL 35 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29M VAL* 4.4 8.3 - - + -
32M TYR 5.5 0.2 - - - +
33M ASN* 5.3 2.0 - - - -
34M TYR* 1.4 83.8 - - - +
36M SER* 1.3 68.7 + - - +
37M TRP* 4.5 8.7 - - + +
50M ILE* 3.7 15.2 - - + +
51M TYR* 3.4 4.3 - - - +
52M GLU* 3.1 28.6 + - - +
53M VAL* 3.8 11.7 + - + +
66M GLY* 6.1 1.3 - - - -
68M LYS* 4.4 26.7 - - - +
73M ALA* 5.5 3.1 - - + -
90M CYS* 5.3 4.0 - - - -
91M SER 2.9 11.0 - - - +
92M SER* 4.0 20.0 - - - +
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Residues in contact with SER 36 (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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34M TYR 5.3 1.1 - - - -
35M VAL* 1.3 80.3 - - - +
37M TRP* 1.3 70.0 + - - +
38M TYR* 3.2 29.8 + - - -
48M VAL* 2.9 31.9 - - - +
50M ILE* 3.3 5.5 + - - -
51M TYR* 4.3 3.7 - - - +
89M TYR 4.1 0.4 - - - -
90M CYS* 3.2 6.8 - - - +
91M SER* 2.9 31.4 + - - -
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Residues in contact with TRP 37 (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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6M GLN* 2.7 37.0 - - - -
20M ILE* 2.8 51.8 - - + -
21M SER 2.9 15.0 - - - -
22M CYS* 4.0 1.8 - - + -
35M VAL* 4.5 6.7 - - + +
36M SER* 1.3 77.5 + - - +
38M TYR* 1.3 58.2 - - - +
48M VAL* 3.4 3.1 - - - +
49M ILE* 2.3 51.5 + - + +
50M ILE* 2.9 26.6 + - + +
66M GLY* 5.4 1.1 - - - -
73M ALA* 4.1 5.8 + - - +
74M SER* 4.4 4.4 + - - -
75M LEU* 2.9 40.0 - - + +
88M TYR* 4.3 4.7 - - + -
89M TYR 3.0 24.5 - - - -
90M CYS* 3.2 19.7 - - + +
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Residues in contact with TYR 38 (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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36M SER* 3.2 28.2 + - - -
37M TRP* 1.3 76.1 - - - +
39M GLN* 1.3 60.3 + - - +
40M GLN 3.9 0.4 - - - -
46M PRO* 4.4 12.6 - - + -
47M LYS 3.6 9.6 - - - +
48M VAL* 3.0 39.6 - - + +
49M ILE* 3.5 2.2 - - - -
87M ASP 3.0 8.7 - - - +
88M TYR* 3.4 4.5 - - - -
89M TYR* 2.8 47.5 + - + +
91M SER* 3.5 21.5 - - - -
99M PHE* 6.0 2.1 - - - -
101M PHE* 4.7 19.2 - + - -
38W PHE* 5.4 8.7 - + - -
99W PHE* 5.9 4.4 - + - -
101W PHE* 4.2 17.7 - + - -
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Residues in contact with GLN 39 (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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38M TYR* 1.3 71.9 - - - +
40M GLN* 1.3 66.6 - - - +
41M HIS* 2.7 37.2 + - - -
46M PRO 2.5 22.5 - - - +
47M LYS* 2.2 59.2 + - + +
49M ILE* 2.7 23.9 - - + +
83M GLU 3.1 4.7 - - - +
86M ALA* 3.4 1.2 - - - +
87M ASP 3.4 2.5 - - - -
88M TYR* 2.9 30.7 + - + +
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Residues in contact with GLN 40 (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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38M TYR 3.8 1.4 + - - -
39M GLN* 1.3 78.7 - - - +
41M HIS* 1.3 54.5 - - - +
42M ALA* 2.8 43.6 + - - +
43M GLY 3.8 0.7 - - - +
44M LYS 4.0 1.2 + - - -
45M ALA* 2.6 37.3 + - - +
46M PRO* 2.9 19.4 - - + +
86M ALA* 2.7 30.7 - - - +
87M ASP* 2.9 23.7 + - + -
89M TYR* 4.3 14.1 + - + -
40W GLN* 2.8 38.6 + - - +
89W PHE* 4.1 1.0 - - - -
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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