Contacts of the strand formed by residues 35 - 40 (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 VAL 35 (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* 6.0 3.4 - - + -
22B CYS* 4.6 2.0 - - - -
29B VAL* 5.7 6.7 - - + -
32B TYR* 4.9 9.2 - - + +
34B TYR* 1.3 87.1 - - - +
36B SER* 1.3 71.8 + - - +
37B TRP* 4.1 11.4 - - - +
50B ILE* 4.4 1.6 - - - +
51B TYR 4.2 0.3 - - - -
52B GLU* 3.6 2.3 + - - -
53B VAL* 2.8 36.1 + - + +
73B ALA* 3.9 29.8 - - + -
90B CYS* 4.5 7.4 - - + -
91B SER 3.6 20.6 - - - +
92B SER* 3.7 12.9 + - - +
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Residues in contact with SER 36 (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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34B TYR* 3.7 9.5 - - - -
35B VAL* 1.3 76.1 - - - +
37B TRP* 1.3 73.4 + - - +
38B TYR* 2.9 14.4 + - - -
50B ILE 3.4 15.5 - - - -
51B TYR* 4.1 2.2 - - - +
90B CYS* 3.5 1.2 - - - -
91B SER* 2.9 29.5 + - - -
1P GLN* 2.9 26.9 + - - -
2P PHE* 3.8 17.5 - - - -
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Residues in contact with TRP 37 (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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6B GLN* 4.5 6.3 - - - -
20B ILE* 3.3 52.5 - - + -
22B CYS* 3.7 16.6 - - + -
35B VAL* 4.1 15.1 - - + +
36B SER* 1.3 85.6 - - - +
38B TYR* 1.3 64.2 + - - +
48B VAL* 3.7 4.5 - - - +
49B ILE* 2.9 39.3 + - + -
50B ILE* 2.9 33.9 + - + +
53B VAL 5.2 2.6 + - - -
66B GLY* 5.2 0.9 - - - -
73B ALA* 3.5 18.8 + - - +
74B SER 3.6 13.1 + - - -
75B LEU* 3.8 26.7 - - + -
88B TYR* 4.7 8.1 - - + -
89B TYR 3.3 24.7 - - - -
90B CYS* 3.8 17.3 - - + -
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Residues in contact with TYR 38 (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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101A PHE* 4.2 6.5 - + - -
36B SER* 2.9 14.8 + - - -
37B TRP* 1.3 76.8 - - - +
39B GLN* 1.3 63.1 + - - +
46B PRO* 5.1 7.9 - - + -
47B LYS 3.1 17.5 - - - +
48B VAL* 3.4 28.5 - - + -
49B ILE* 4.1 4.7 - - - +
88B TYR* 3.2 13.5 - - - +
89B TYR* 2.8 53.7 + - + +
91B SER* 3.3 23.1 - - - -
101B PHE* 3.9 15.7 - + + -
0P ACE 2.8 36.2 + - + -
1P GLN* 2.9 24.1 + - - -
2P PHE* 3.2 6.8 - + - -
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Residues in contact with GLN 39 (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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38B TYR* 1.3 76.4 - - - +
40B GLN* 1.3 59.8 + - - +
41B HIS* 4.0 20.8 + - - +
45B ALA 4.4 1.0 - - - +
46B PRO* 3.3 4.9 - - - +
47B LYS* 2.9 57.6 + - + +
49B ILE* 3.9 19.1 - - + -
64B PHE* 4.8 5.4 - - - -
83B GLU 5.0 1.2 - - - +
84B ASP* 3.8 7.7 + - - +
86B ALA* 3.8 14.5 - - - +
87B ASP 3.5 5.8 - - - +
88B TYR* 3.2 38.2 + - + -
89B TYR* 5.6 0.2 - - - -
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Residues in contact with GLN 40 (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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40A GLN* 3.3 18.0 + - - +
89A TYR* 3.1 40.4 + - - -
39B GLN* 1.3 73.2 - - - +
41B HIS* 1.3 59.2 + - - +
42B ALA 5.5 4.9 - - - +
43B GLY 6.1 0.4 - - - -
44B LYS 4.2 11.6 + - - +
45B ALA 5.1 1.1 - - - -
46B PRO* 4.0 21.9 - - + +
86B ALA* 4.0 1.6 - - - -
87B ASP* 2.8 45.7 + - + +
89B TYR* 3.0 39.5 + - + -
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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