Contacts of the helix formed by residues 102 - 118 (chain B) 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 ASN 102 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100B GLN* 3.3 6.0 + - - +
101B ARG* 1.3 87.4 - - - +
103B LEU* 1.3 69.1 + - - +
104B ASN* 4.4 7.9 - - + +
105B TYR* 5.0 4.0 - - + +
106B PHE* 3.5 7.0 + - - +
954B TRP* 3.5 15.7 - - - -
975B TYR* 5.0 4.8 - - - -
979B PHE* 6.0 0.7 - - - -
980B GLY 5.1 0.2 - - - -
982B SER* 2.9 32.2 - - - +
983B ARG* 3.2 49.1 - - - +
984B PRO* 3.8 3.3 - - - +
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Residues in contact with LEU 103 (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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102B ASN* 1.3 76.6 - - - +
104B ASN* 1.3 71.3 + - - +
106B PHE* 2.8 30.7 + - + +
107B SER* 2.8 30.2 + - - +
429B SER 5.9 0.4 - - - +
430B HIS 5.1 0.2 - - - +
431B LEU* 3.3 48.5 - - + +
957B MET* 5.9 1.6 - - + -
972B VAL* 4.6 13.9 - - + +
975B TYR* 5.1 14.8 - - + +
976B PHE* 5.3 3.1 - - + +
979B PHE 5.4 0.4 + - - -
980B GLY* 3.3 25.0 + - - +
981B LEU* 3.7 17.0 - - + -
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Residues in contact with ASN 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ASN* 3.6 5.8 - - + +
103B LEU* 1.3 80.5 - - - +
105B TYR* 1.3 56.5 + - - +
107B SER* 2.5 18.2 + - - -
108B ASN* 2.5 36.2 + - - +
981B LEU* 3.3 48.5 + - - +
982B SER 4.9 0.4 - - - +
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Residues in contact with TYR 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B VAL* 4.1 21.8 - - + +
98B SER* 4.1 19.5 - - - -
100B GLN* 3.1 61.7 - - + +
102B ASN* 5.0 4.6 - - + +
104B ASN* 1.3 80.0 - - - +
106B PHE* 1.3 60.4 + + + +
108B ASN* 3.8 5.2 - - + +
109B ALA* 2.8 48.9 + - + +
954B TRP* 5.2 1.8 - + - -
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Residues in contact with PHE 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B VAL* 4.9 10.1 - - + -
102B ASN 3.5 13.4 + - - +
103B LEU* 2.8 19.5 + - + +
105B TYR* 1.3 78.1 - + - +
107B SER* 1.3 61.6 + - - +
109B ALA* 4.4 3.6 - - + -
110B TYR* 2.8 71.1 + + + +
954B TRP* 3.6 25.6 - + + -
957B MET* 3.5 49.4 - - + -
958B ASN* 3.9 21.3 - - - -
968B ARG* 5.5 4.5 - - + -
972B VAL* 4.3 14.1 - - + -
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Residues in contact with SER 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LEU* 2.8 30.6 + - - +
104B ASN* 2.5 30.1 + - - -
106B PHE* 1.3 78.1 - - - +
108B ASN* 1.3 63.2 + - - -
110B TYR* 3.8 4.4 - - - +
111B ALA* 2.8 31.1 + - - +
431B LEU 4.5 9.2 + - - -
432B HIS* 5.0 10.8 - - - -
433B PHE* 5.3 4.3 - - - +
440B THR* 5.8 3.3 - - - +
972B VAL* 6.1 2.9 - - - -
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Residues in contact with ASN 108 (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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104B ASN* 2.5 33.1 + - - +
105B TYR* 4.0 5.2 - - + +
107B SER* 1.3 85.3 + - - +
109B ALA* 1.3 58.2 + - - +
111B ALA* 3.3 6.7 + - - +
112B ALA* 2.9 30.3 + - - +
424B LYS* 5.1 19.9 - - - +
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Residues in contact with ALA 109 (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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93B VAL* 5.8 6.3 - - + -
105B TYR* 2.8 41.3 + - + +
106B PHE* 3.9 5.6 - - + +
108B ASN* 1.3 76.4 - - - +
110B TYR* 1.3 58.7 + - - +
112B ALA* 3.4 5.6 + - - +
113B ALA* 2.8 30.4 + - - +
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Residues in contact with TYR 110 (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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90B THR* 4.4 8.8 - - - +
91B LEU 5.6 3.4 - - - -
106B PHE* 2.8 49.1 + + + +
107B SER* 3.9 3.8 - - - +
109B ALA* 1.3 73.6 - - - +
111B ALA* 1.3 62.5 + - - +
113B ALA* 4.0 6.5 - - + -
114B VAL* 2.9 56.2 + - + +
437B HIS* 6.1 1.1 - + - -
439B HIS 4.1 18.2 + - - -
440B THR* 5.6 9.9 - - + -
965B TRP* 3.2 29.7 - + - -
968B ARG* 3.3 41.4 + - + +
969B CYS* 6.0 1.5 - - - -
972B VAL* 5.9 2.9 - - + -
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Residues in contact with ALA 111 (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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107B SER 2.8 19.5 + - - +
108B ASN* 3.5 7.4 - - - +
109B ALA 3.2 0.2 - - - -
110B TYR* 1.3 79.3 - - - +
112B ALA* 1.3 58.2 + - - +
114B VAL* 4.5 1.4 - - - +
115B SER* 2.9 31.5 + - - -
433B PHE* 4.0 42.5 - - + -
437B HIS* 5.7 4.5 + - - -
440B THR* 5.4 5.6 - - + +
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Residues in contact with ALA 112 (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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108B ASN 2.9 17.0 + - - +
109B ALA* 3.8 5.2 - - - +
111B ALA* 1.3 75.0 - - - +
113B ALA* 1.3 57.5 + - - +
115B SER* 2.5 24.0 + - - +
116B ALA* 2.9 17.0 + - - +
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Residues in contact with ALA 113 (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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89B PRO* 4.3 21.9 - - + +
109B ALA 2.8 18.2 + - - +
110B TYR* 3.4 12.1 - - + +
112B ALA* 1.3 77.4 - - - +
114B VAL* 1.3 61.8 + - + +
116B ALA* 3.0 10.3 + - - +
117B VAL* 2.9 29.0 + - - +
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Residues in contact with VAL 114 (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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90B THR* 5.0 7.0 - - + -
110B TYR* 2.9 50.1 + - + +
111B ALA* 4.5 1.6 - - - +
113B ALA* 1.3 76.7 - - + +
115B SER* 1.3 64.1 + - - +
117B VAL* 3.4 17.4 - - + +
118B ASP* 3.0 26.6 + - - +
187B ARG* 5.0 2.5 - - - +
437B HIS* 3.3 30.3 - - + +
965B TRP* 3.6 28.3 - - + -
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Residues in contact with SER 115 (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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111B ALA 2.9 15.8 + - - -
112B ALA* 2.5 28.8 + - - -
114B VAL* 1.3 76.8 - - - +
116B ALA* 1.3 59.6 + - - +
118B ASP* 3.2 30.2 + - - +
120B ASP 5.9 0.3 - - - -
121B ALA* 5.8 0.5 - - - +
123B ASN* 4.3 2.4 + - - -
433B PHE* 6.2 4.3 - - - -
436B LYS* 5.9 10.5 - - - -
437B HIS* 4.6 4.6 - - - -
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Residues in contact with ALA 116 (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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64B LYS* 3.5 1.2 + - - -
89B PRO* 5.9 2.9 - - + -
112B ALA 2.9 14.7 + - - +
113B ALA* 3.0 11.2 + - - +
115B SER* 1.3 74.7 + - - +
117B VAL* 1.3 65.5 + - + +
118B ASP 3.2 7.4 - - - +
123B ASN* 3.3 27.2 - - - +
124B GLY 4.5 2.6 + - - +
125B GLU* 4.5 1.4 - - - +
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Residues in contact with VAL 117 (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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64B LYS* 2.5 22.9 + - - -
66B ASN* 2.9 25.1 + - - +
68B LYS* 6.2 1.6 - - + -
89B PRO* 3.7 14.1 - - + -
90B THR* 3.5 29.8 - - - +
113B ALA 2.9 20.7 + - - +
114B VAL* 3.2 18.6 + - + +
116B ALA* 1.3 73.4 - - - +
118B ASP* 1.3 57.4 + - - +
125B GLU* 3.4 26.2 - - - +
187B ARG* 3.4 23.3 - - - +
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Residues in contact with ASP 118 (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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64B LYS* 3.3 0.2 - - - -
114B VAL 3.0 15.1 + - - +
115B SER* 3.2 16.6 - - - +
116B ALA 3.2 0.6 - - - +
117B VAL* 1.3 75.4 - - - +
119B PRO* 1.3 55.6 - - - -
120B ASP* 3.1 12.0 + - + +
123B ASN* 2.3 33.3 + - - -
187B ARG* 2.4 30.8 + - - -
194B ASP* 3.0 17.0 - - - +
436B LYS 4.8 3.3 - - - +
437B HIS* 3.3 26.7 + - - -
439B HIS* 5.8 0.3 - - - -
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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