Contacts of the helix formed by residues 36 - 41 (chain S) in PDB entry 6MZL
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 LEU 36 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129P PHE* 3.6 27.8 - - + -
162P VAL* 3.8 15.3 - - + -
32S PHE* 2.7 33.2 + - + +
33S SER* 4.9 1.6 - - - +
35S GLU* 1.3 70.8 - - - +
37S ARG* 1.3 53.7 + - - +
38S CYS 3.3 0.2 - - - -
39S MET* 3.0 6.4 + - - -
40S MET* 2.6 45.4 + - + +
54S VAL* 4.1 8.7 - - + +
57S LEU* 3.6 35.0 - - + +
58S GLU* 3.6 32.5 - - + +
61S VAL* 4.3 4.5 - - + -
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Residues in contact with ARG 37 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33S SER* 3.6 30.9 + - - +
34S LYS* 3.7 8.5 + - - +
35S GLU 3.3 0.2 - - - -
36S LEU* 1.3 76.2 - - - +
38S CYS* 1.3 59.9 + - - +
40S MET* 3.2 10.6 + - - +
41S TYR* 3.0 29.6 + - - +
47S GLN 4.7 6.5 - - - +
48S ASN* 3.9 14.5 - - - +
49S PRO* 3.0 49.0 + - + +
51S THR* 3.7 25.5 + - - +
54S VAL* 3.6 20.5 - - + +
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Residues in contact with CYS 38 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123P MET* 3.1 60.9 - - + +
127P SER* 3.7 6.0 - - - -
34S LYS* 3.6 18.8 + - - +
35S GLU* 3.5 12.3 + - - +
37S ARG* 1.3 77.2 - - - +
39S MET* 1.3 57.4 + - - +
41S TYR* 4.2 6.1 - - - +
42S GLY 3.8 5.9 + - - -
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Residues in contact with MET 39 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123P MET 4.8 0.2 - - - -
127P SER* 3.5 27.8 - - - +
128P ALA* 3.8 22.7 - - - +
129P PHE* 3.7 33.2 - - + +
155P SER 5.7 0.2 - - - +
159P LYS* 3.7 25.8 - - + -
162P VAL* 3.7 33.7 - - + +
35S GLU 3.2 7.8 + - - +
36S LEU* 3.0 11.7 + - + +
38S CYS* 1.3 78.4 - - - +
40S MET* 1.3 63.6 + - - +
41S TYR 3.4 0.2 - - - -
42S GLY* 3.5 5.2 + - - +
43S PHE* 3.2 36.8 - - + -
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Residues in contact with MET 40 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162P VAL* 5.3 0.2 - - + -
166P VAL* 3.7 14.0 - - + +
187P MET* 3.7 23.1 - - + -
36S LEU* 2.6 26.4 + - + +
37S ARG* 3.2 8.3 + - - +
39S MET* 1.3 74.8 - - - +
41S TYR* 1.3 62.6 + - - +
43S PHE 3.6 4.0 + - - -
45S ASP* 3.2 35.1 + - + +
49S PRO* 3.9 18.6 - - + -
53S SER* 3.8 25.4 - - - -
54S VAL* 3.6 30.3 - - + -
57S LEU* 3.7 26.9 - - + -
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Residues in contact with TYR 41 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116P GLU* 3.5 16.2 + - - +
119P ASN* 3.4 42.3 + - - +
120P ARG* 3.2 59.3 + - - +
123P MET* 3.6 24.7 - - + -
37S ARG 3.0 15.1 + - - +
38S CYS* 4.7 4.5 - - - +
40S MET* 1.3 76.9 - - - +
42S GLY* 1.3 61.1 + - - +
44S GLY 3.1 12.0 + - - -
45S ASP 3.2 20.4 - - - -
46S ASP 3.5 13.1 + - - +
47S GLN* 3.4 40.7 + - + -
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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