Contacts of the helix formed by residues 114 - 126 (chain P) 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 SER 114 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113P PHE* 1.3 87.7 - - - +
115P GLU* 1.3 64.1 + - - +
116P GLU* 3.9 6.1 + - - +
117P GLN* 3.3 34.9 + - - +
118P LEU* 3.3 17.5 + - - +
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Residues in contact with GLU 115 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114P SER* 1.3 72.1 - - - +
116P GLU* 1.3 59.7 + - - +
118P LEU* 3.2 21.0 - - + +
119P ASN* 3.1 24.8 + - - +
338T THR* 3.3 49.0 + - + +
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Residues in contact with GLU 116 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114P SER* 3.3 7.0 + - - +
115P GLU* 1.3 77.6 - - - +
117P GLN* 1.3 58.6 + - + +
119P ASN* 3.3 5.3 + - + +
120P ARG* 2.9 62.4 + - - +
41S TYR* 3.5 11.0 + - - +
46S ASP* 5.7 0.7 - - - +
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Residues in contact with GLN 117 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113P PHE* 3.6 26.8 - - + +
114P SER* 3.3 23.2 + - - +
115P GLU 3.4 0.4 - - - -
116P GLU* 1.3 75.1 - - + +
118P LEU* 1.3 58.3 + - - +
120P ARG* 4.0 8.5 - - - +
121P TYR* 2.9 33.6 + - - +
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Residues in contact with LEU 118 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113P PHE* 4.9 7.7 - - + -
114P SER 3.3 10.3 + - - +
115P GLU* 3.2 24.0 - - + +
117P GLN* 1.3 77.7 - - - +
119P ASN* 1.3 75.8 + - + +
121P TYR* 4.1 2.2 - - - +
122P GLU* 3.1 26.2 + - - +
269T ARG* 3.4 54.6 - - + +
336T ARG 3.3 25.1 - - - +
337T LYS* 3.8 17.0 - - + -
338T THR 4.1 7.2 - - - +
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Residues in contact with ASN 119 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115P GLU 3.1 13.8 + - - +
116P GLU* 3.3 6.5 + - - +
118P LEU* 1.3 83.2 - - + +
120P ARG* 1.3 57.9 + - - +
122P GLU 3.6 0.2 + - - -
123P MET* 3.0 27.9 + - - +
41S TYR* 3.4 23.1 + - - +
47S GLN* 3.6 29.0 + - - +
337T LYS* 3.4 31.9 + - - +
338T THR 4.3 16.7 + - - +
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Residues in contact with ARG 120 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116P GLU* 2.9 48.9 + - - +
117P GLN* 4.0 6.6 - - - +
119P ASN* 1.3 76.5 - - - +
121P TYR* 1.3 60.3 + - - +
123P MET 3.5 0.3 + - - -
124P TYR 2.9 21.8 + - - -
41S TYR* 3.2 50.6 + - + +
42S GLY* 3.4 14.3 - - - +
43S PHE 5.0 0.4 - - - -
44S GLY* 3.2 28.8 + - - +
45S ASP 2.4 32.1 + - - -
46S ASP* 5.3 2.0 - - - +
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Residues in contact with TYR 121 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117P GLN 2.9 18.5 + - - +
118P LEU* 4.3 2.0 - - - +
120P ARG* 1.3 73.9 - - - +
122P GLU* 1.3 64.3 + - - +
124P TYR* 3.3 36.9 - + + +
125P ARG* 2.9 30.4 + - + +
42S GLY 5.1 0.2 - - - -
269T ARG* 6.4 2.0 - - + -
271T GLU* 3.7 40.7 - - + +
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Residues in contact with GLU 122 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118P LEU 3.1 18.1 + - - +
121P TYR* 1.3 77.9 - - - +
123P MET* 1.3 59.7 + - - +
125P ARG* 2.3 46.9 + - - -
126P ARG* 3.1 27.9 + - - +
267T PRO* 4.8 0.9 - - + -
268T ILE 3.1 25.0 - - - +
269T ARG* 3.3 19.2 - - + +
270T LEU 3.7 0.2 + - - -
271T GLU 5.0 0.2 + - - -
306T VAL* 3.4 18.9 - - + +
337T LYS* 3.6 31.4 - - + -
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Residues in contact with MET 123 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119P ASN* 3.0 18.1 + - - +
120P ARG 3.9 2.0 - - - +
122P GLU* 1.3 72.3 - - - +
124P TYR* 1.3 65.9 + - - +
126P ARG 4.4 0.9 - - - +
127P SER* 3.3 14.9 + - - +
38S CYS* 3.1 64.2 - - - +
41S TYR* 3.6 31.4 - - + -
42S GLY* 3.9 3.5 - - - -
47S GLN* 6.4 0.7 - - - +
337T LYS* 3.3 27.4 - - - +
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Residues in contact with TYR 124 (chain P).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120P ARG 2.9 9.8 + - - +
121P TYR* 3.3 51.4 - + + +
123P MET* 1.3 75.9 - - - +
125P ARG* 1.3 75.0 - - + +
127P SER* 3.1 12.0 + - - -
159P LYS* 3.0 32.7 + - - -
42S GLY* 3.2 23.3 - - - +
43S PHE* 3.5 45.3 - + - -
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Residues in contact with ARG 125 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121P TYR* 2.9 20.9 + - + +
122P GLU* 2.3 42.9 + - - +
124P TYR* 1.3 89.6 - - + +
126P ARG* 1.3 88.8 + - - +
159P LYS* 3.5 12.8 + - - +
268T ILE 3.6 2.0 + - - -
270T LEU* 3.4 36.8 - - - +
271T GLU* 4.0 20.6 - - - +
283T TYR* 2.4 58.4 + - + +
285T PRO* 5.3 9.9 - - + +
306T VAL* 4.4 5.1 - - - +
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Residues in contact with ARG 126 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A GLU* 4.7 8.5 + - - -
122P GLU 3.1 10.7 + - - +
123P MET* 5.2 0.9 - - - -
125P ARG* 1.3 107.6 - - - +
127P SER* 1.3 64.5 + - - +
128P ALA* 3.5 5.6 + - - +
270T LEU* 4.2 0.8 - - - +
283T TYR* 4.9 0.4 - - - -
289T PRO* 2.7 55.1 + - - +
290T GLY* 3.4 2.2 - - - -
304T ILE 3.7 1.0 + - - -
305T PHE* 3.3 36.4 - - - +
306T VAL* 3.4 57.5 - - + +
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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