Contacts of the strand formed by residues 36 - 42 (chain H) in PDB entry 6CMO
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 36 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32H PHE* 6.3 0.2 - - - -
35H SER* 1.3 75.9 - - - +
37H ILE* 1.3 71.9 + - - +
38H HIS* 2.7 25.6 + - - -
53H SER* 4.4 0.2 - - - -
54H ILE 3.4 16.4 - - - -
55H TYR* 3.7 10.3 - - - -
56H SER* 5.6 0.2 - - - -
101H ARG* 3.5 2.9 - - - +
102H TYR 2.7 39.1 + - - -
104H TRP* 3.2 23.0 + - - -
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Residues in contact with ILE 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H LEU* 4.5 8.5 - - + -
25H CYS* 4.7 5.4 - - + +
27H ALA* 5.9 0.4 - - + -
30H PHE* 4.4 21.3 - - + -
32H PHE* 3.5 30.5 - - + -
35H SER* 4.6 2.0 - - - +
36H SER* 1.3 84.5 - - - +
38H HIS* 1.3 64.0 + - - +
39H TRP* 4.3 18.0 - - - +
53H SER* 3.4 4.2 + - - -
54H ILE* 3.0 36.3 + - + +
82H ALA* 4.8 11.4 - - + -
99H CYS* 3.8 25.6 - - - -
100H ALA 3.3 6.5 - - - +
101H ARG* 4.3 13.7 - - + -
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Residues in contact with HIS 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H SER* 2.7 27.6 + - - -
37H ILE* 1.3 74.4 - - - +
39H TRP* 1.3 63.5 + - - +
40H VAL* 5.4 2.5 - - + -
50H TRP* 3.7 16.3 + - + +
52H ALA 3.9 2.2 - - - -
53H SER* 3.1 31.5 + - - -
55H TYR* 4.1 9.0 - + - -
98H TYR 3.2 4.3 - - - +
99H CYS* 3.7 3.1 - - - -
100H ALA* 2.7 46.4 + - + +
102H TYR* 3.4 30.6 - - + +
104H TRP* 3.9 5.0 + + - -
118H MET* 3.9 12.6 - - + -
97L ILE* 4.0 22.6 - - + +
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Residues in contact with TRP 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H GLU* 4.2 18.2 - - + -
10H SER 5.3 0.2 - - - -
23H LEU* 4.5 15.0 - - + -
24H SER* 3.6 30.7 - - - -
25H CYS* 3.6 31.4 - - + -
37H ILE* 4.3 14.7 - - + +
38H HIS* 1.3 82.8 - - - +
40H VAL* 1.3 60.9 + - - +
50H TRP* 3.4 16.8 - - - -
51H VAL* 3.4 18.5 - - + +
52H ALA 3.2 15.2 + - - +
53H SER* 5.4 1.1 - - - -
54H ILE* 4.9 13.4 - - + +
82H ALA* 5.0 4.1 - - + +
83H TYR 5.4 0.4 - - - -
84H LEU* 3.5 37.3 - - + +
97H TYR* 3.9 35.0 - + + -
98H TYR 3.5 15.0 - - - -
99H CYS* 4.6 2.5 - - + -
125H THR* 6.4 0.9 - - + -
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Residues in contact with VAL 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H HIS* 5.4 4.3 - - + -
39H TRP* 1.3 80.4 - - - +
41H ARG* 1.3 62.2 + - - +
48H LEU* 3.7 22.2 - - + -
49H GLU 3.3 10.3 - - - +
50H TRP* 3.9 16.4 - - + +
51H VAL* 4.4 0.4 - - - -
96H VAL 3.3 13.6 - - - +
97H TYR* 3.4 18.0 - - - -
98H TYR* 3.6 29.7 + - + +
100H ALA* 5.8 1.3 - - + -
118H MET* 6.3 1.1 - - + -
121H TRP* 4.2 15.7 - - + -
99L PHE* 3.7 27.8 - - + -
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Residues in contact with ARG 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H VAL* 1.3 72.7 - - - +
42H GLN* 1.3 58.9 + - - +
43H ALA* 3.8 10.1 + - - +
48H LEU* 3.5 4.9 - - - +
49H GLU* 2.6 73.9 + - + +
51H VAL* 3.7 26.8 - - + +
67H VAL* 5.7 4.7 - - - +
71H PHE* 6.4 2.0 - - - -
92H GLU 3.1 26.1 + - - -
93H ASP* 3.6 27.7 + - - +
94H THR 4.0 7.7 + - - -
95H ALA* 3.7 12.3 - - + +
96H VAL 3.9 1.8 - - - -
97H TYR* 3.6 29.5 + - + -
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Residues in contact with GLN 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41H ARG* 1.3 70.3 - - - +
43H ALA* 1.3 90.1 + - - +
44H PRO* 3.8 7.5 - - - +
45H GLY 4.6 2.6 - - - +
46H LYS 3.6 9.9 + - - -
47H GLY 3.8 3.1 - - - +
48H LEU* 3.7 31.2 - - + -
95H ALA* 3.3 6.9 - - - +
96H VAL* 3.1 55.3 + - + +
98H TYR* 5.0 13.7 - - + +
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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