Contacts of the helix formed by residues 105 - 118 (chain K) 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 ASP 105 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103K ASN* 3.1 24.2 + - - +
104K VAL* 1.3 86.3 - - - +
106K THR* 1.3 60.7 + - + +
107K LEU 3.2 0.2 - - - -
108K PRO* 3.3 15.6 - - - +
109K ALA* 4.6 2.9 + - - +
116O LEU* 4.3 18.0 - - - +
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Residues in contact with THR 106 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102K PHE* 3.2 15.6 - - - -
103K ASN* 3.1 31.4 + - + +
105K ASP* 1.3 77.1 - - + +
107K LEU* 1.3 53.9 + - - +
108K PRO 3.4 0.9 - - - -
109K ALA* 3.2 11.2 + - + -
110K TYR* 2.6 36.5 + - - +
161O LYS* 3.3 23.0 + - - +
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Residues in contact with LEU 107 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97K LEU* 5.2 5.2 - - + -
102K PHE* 3.5 27.6 - - + -
104K VAL* 3.0 39.3 + - + +
106K THR* 1.3 77.8 + - - +
108K PRO* 1.3 62.9 - - + +
110K TYR* 4.0 6.0 - - + +
111K ALA* 3.2 15.8 + - - +
116O LEU* 5.7 0.4 - - + -
119O PHE* 3.6 24.9 - - + -
154O LEU* 3.7 27.4 - - + -
157O LEU* 4.7 14.0 - - + +
158O ALA* 4.5 22.4 - - - +
161O LYS* 5.2 4.0 - - + -
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Residues in contact with PRO 108 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104K VAL 3.9 3.8 - - - +
105K ASP* 3.3 17.3 - - - +
107K LEU* 1.3 93.4 - - + +
109K ALA* 1.3 56.2 + - - +
111K ALA* 2.8 27.3 + - + +
112K LYS* 3.5 7.1 + - - +
116K ARG* 5.2 0.9 + - - -
115O PRO* 4.7 9.0 - - + +
116O LEU* 5.3 3.1 - - + -
119O PHE* 3.6 40.8 - - + -
122O GLN* 4.7 6.3 - - - +
126O TYR* 4.5 1.3 + - - +
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Residues in contact with ALA 109 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105K ASP 4.6 2.0 + - - +
106K THR* 3.2 16.5 + - + +
108K PRO* 1.3 79.8 - - - +
110K TYR* 1.3 57.6 + - - +
112K LYS* 2.9 41.4 + - + +
113K ARG* 3.7 4.5 + - - +
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Residues in contact with TYR 110 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44K LEU* 3.8 8.8 - - - +
47K GLU* 6.0 1.7 - - + +
106K THR 2.6 22.3 + - - +
107K LEU* 4.1 8.3 - - + +
109K ALA* 1.3 69.8 - - - +
111K ALA* 1.3 53.9 + - - +
113K ARG* 2.9 43.0 + - + +
114K SER* 2.7 49.6 + - - -
157O LEU* 3.7 12.1 - - + -
160O GLN* 3.0 25.0 + - + +
161O LYS* 3.5 47.5 - - + +
164O SER* 2.3 39.3 + - - -
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Residues in contact with ALA 111 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107K LEU 3.2 11.2 + - - +
108K PRO* 2.8 20.5 + - + +
110K TYR* 1.3 76.7 - - - +
112K LYS* 1.3 58.3 + - - +
114K SER* 3.0 21.5 + - - +
115K GLN* 3.3 12.1 + - + +
116K ARG* 3.5 20.2 - - - +
119O PHE* 5.0 0.4 - - + -
126O TYR* 3.7 32.5 - - + +
157O LEU* 5.5 4.0 - - + +
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Residues in contact with LYS 112 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108K PRO 4.3 4.7 - - - +
109K ALA* 2.9 26.3 + - + +
111K ALA* 1.3 75.9 - - - +
113K ARG* 1.3 57.9 + - + +
116K ARG* 3.4 42.0 - - - +
117K MET* 3.3 22.4 - - - +
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Residues in contact with ARG 113 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47K GLU* 4.2 14.5 - - + +
109K ALA 4.6 4.9 - - - +
110K TYR* 2.9 46.3 + - + +
111K ALA 3.8 0.2 - - - -
112K LYS* 1.3 79.9 - - + +
114K SER* 1.3 62.9 + - - +
117K MET* 3.3 36.3 + - - +
118K VAL* 3.8 8.1 + - - +
161O LYS* 4.6 7.8 - - - +
164O SER* 4.2 7.2 - - - -
165O ASP* 4.4 4.8 + - - -
168O ASN* 4.1 24.9 + - - +
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Residues in contact with SER 114 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44K LEU* 6.4 1.3 - - - -
110K TYR* 2.7 31.1 + - - -
111K ALA* 3.0 18.0 + - - -
113K ARG* 1.3 77.3 - - - +
115K GLN* 1.3 79.1 + - - +
116K ARG 3.2 1.2 + - - -
118K VAL* 3.5 18.2 + - - +
129O THR* 3.2 15.6 + - - -
157O LEU* 3.5 11.5 - - - +
160O GLN* 3.3 23.1 - - - -
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Residues in contact with GLN 115 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111K ALA* 3.3 5.6 + - - +
114K SER* 1.3 88.7 + - - +
116K ARG* 1.3 63.3 + - + +
117K MET 3.8 0.2 - - - -
118K VAL 4.4 6.5 - - - +
120K THR* 5.9 1.1 - - - -
126O TYR* 3.2 39.3 - - + +
127O THR* 2.8 39.9 + - - +
128O PRO* 3.3 28.0 - - + +
129O THR* 4.3 3.4 - - - -
153O ARG* 5.2 0.2 - - - +
157O LEU* 3.4 23.5 - - + +
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Residues in contact with ARG 116 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108K PRO 5.2 0.6 + - - -
111K ALA* 3.5 19.5 + - - +
112K LYS* 3.4 50.5 - - - +
114K SER 3.2 0.8 - - - -
115K GLN* 1.3 85.9 - - + +
117K MET* 1.3 64.6 + - + +
118K VAL 3.9 0.7 - - - -
126O TYR* 4.7 18.4 + - - -
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Residues in contact with MET 117 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47K GLU* 3.1 38.8 - - - +
112K LYS 3.3 21.5 - - - +
113K ARG* 3.3 24.9 + - - +
116K ARG* 1.3 82.6 - - + +
118K VAL* 1.3 58.3 + - - +
119K ILE* 4.4 1.2 + - - +
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Residues in contact with VAL 118 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43K SER* 3.9 26.7 - - - +
44K LEU* 4.8 10.5 - - + -
47K GLU* 3.3 41.3 - - + +
113K ARG 4.0 7.0 - - - +
114K SER* 3.5 20.8 + - - +
115K GLN* 4.4 8.8 - - - +
116K ARG 5.1 0.3 - - - -
117K MET* 1.3 76.5 + - - +
119K ILE* 1.3 74.9 + - - +
120K THR* 3.7 2.8 + - - -
129O THR* 3.8 19.8 + - + -
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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