Contacts of the helix formed by residues 104 - 116 (chain H) in PDB entry 4MNE
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 LYS 104 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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542G HIS 3.8 17.7 + - - +
543G ILE* 3.3 27.2 - - - +
545G GLU* 3.0 30.5 + - - +
103H ILE* 1.3 76.7 - - - +
105H PRO* 1.3 69.5 - - + +
106H ALA* 4.4 6.3 - - + +
107H ILE* 3.4 30.2 + - + +
108H ARG* 3.0 24.8 + - - +
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Residues in contact with PRO 105 (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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543G ILE* 5.1 9.4 - - + +
103H ILE 4.2 1.6 - - - +
104H LYS* 1.3 86.2 - - + +
106H ALA* 1.3 67.7 + - - +
108H ARG* 3.0 43.2 + - - +
109H ASN* 2.9 30.5 + - - +
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Residues in contact with ALA 106 (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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104H LYS* 3.4 4.8 - - + +
105H PRO* 1.3 80.0 - - - +
107H ILE* 1.3 68.4 + - + +
109H ASN* 3.2 10.8 + - - +
110H GLN* 3.1 23.2 + - - +
113H ARG* 5.6 0.2 + - - -
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Residues in contact with ILE 107 (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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103H ILE* 4.2 14.4 - - + -
104H LYS* 3.4 43.3 + - + +
106H ALA* 1.3 79.3 - - + +
108H ARG* 1.3 63.2 + - - +
110H GLN* 3.2 12.9 + - - +
111H ILE* 3.2 22.1 + - + +
214H GLN* 3.8 31.9 - - + +
218H SER* 3.7 22.7 - - - +
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Residues in contact with ARG 108 (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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103H ILE* 3.8 30.0 + - + -
104H LYS 3.0 12.2 + - - +
105H PRO* 3.0 41.2 + - - +
107H ILE* 1.3 76.2 - - - +
109H ASN* 1.3 77.3 + - - +
111H ILE* 3.3 6.9 + - - +
112H ILE* 3.2 25.4 + - + +
134H TYR* 3.3 67.1 + - + +
139H ILE* 4.5 3.4 - - + +
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Residues in contact with ASN 109 (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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105H PRO* 2.9 22.7 + - - +
106H ALA* 3.2 10.8 + - - +
108H ARG* 1.3 89.0 + - - +
110H GLN* 1.3 56.1 + - - +
112H ILE* 2.9 11.8 + - - +
113H ARG* 2.8 38.3 + - - +
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Residues in contact with GLN 110 (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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106H ALA 3.1 13.5 + - - +
107H ILE* 3.2 14.9 + - - +
109H ASN* 1.3 76.9 - - - +
111H ILE* 1.3 52.2 + - - +
113H ARG* 3.6 32.1 + - - +
114H GLU* 2.7 68.4 + - + +
214H GLN* 3.4 32.2 + - + +
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Residues in contact with ILE 111 (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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101H LEU* 4.2 6.3 - - + -
103H ILE* 3.9 26.9 - - + -
107H ILE* 3.2 12.6 + - + +
108H ARG* 3.5 7.0 - - - +
110H GLN* 1.3 75.3 - - - +
112H ILE* 1.3 58.5 + - - +
114H GLU* 3.2 2.3 + - - +
115H LEU* 2.9 47.1 + - + +
139H ILE* 4.4 16.4 - - + -
212H SER* 3.9 7.4 + - - -
214H GLN* 3.9 10.5 - - + +
215H LEU* 3.8 51.4 - - + +
218H SER* 4.4 6.5 - - - +
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Residues in contact with ILE 112 (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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108H ARG* 3.3 16.2 - - + +
109H ASN* 2.9 11.0 + - - +
111H ILE* 1.3 72.7 - - - +
113H ARG* 1.3 67.9 + - - +
115H LEU* 3.0 15.3 + - + +
116H GLN* 3.2 26.4 + - - +
132H ALA* 3.3 24.5 - - + +
133H PHE* 3.5 35.9 - - - +
134H TYR* 3.9 9.2 - - + +
139H ILE* 4.2 19.5 - - + -
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Residues in contact with ARG 113 (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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109H ASN* 2.8 21.4 + - - +
110H GLN* 3.6 41.9 + - - +
112H ILE* 1.3 72.8 - - - +
114H GLU* 1.3 66.9 + - + +
116H GLN* 3.1 26.0 + - - +
117H VAL* 4.4 2.6 + - - +
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Residues in contact with GLU 114 (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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110H GLN* 2.7 60.7 + - + +
111H ILE 3.7 0.2 - - - +
113H ARG* 1.3 78.5 - - + +
115H LEU* 1.3 60.5 + - - +
116H GLN 3.3 0.7 + - - -
117H VAL* 3.5 22.0 + - - +
211H VAL* 3.9 10.5 - - - +
212H SER* 2.4 38.6 + - - +
213H GLY* 2.9 17.7 + - - -
214H GLN* 3.0 6.9 + - - +
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Residues in contact with LEU 115 (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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111H ILE* 2.9 41.7 + - + +
112H ILE* 3.0 8.0 + - - +
114H GLU* 1.3 72.1 - - - +
116H GLN* 1.3 62.1 + - - +
117H VAL 3.0 5.4 - - - -
118H LEU* 3.0 33.0 + - + +
129H PHE* 3.8 9.0 - - + -
132H ALA* 3.7 30.1 - - + -
139H ILE* 4.1 14.4 - - + -
141H ILE* 3.8 25.6 - - + -
211H VAL* 4.1 11.7 - - + -
212H SER* 4.4 4.7 - - - -
215H LEU* 4.6 1.8 - - + -
903H 573 3.9 22.9 - - + +
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Residues in contact with GLN 116 (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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112H ILE* 3.2 31.9 + - + +
113H ARG* 3.2 21.3 - - - +
114H GLU 3.1 0.4 - - - -
115H LEU* 1.3 79.5 - - - +
117H VAL* 1.3 61.6 + - + +
118H LEU 3.1 1.0 + - - -
119H HIS* 3.1 50.5 + - + +
120H GLU* 4.5 1.6 + - - -
129H PHE* 4.6 3.3 - - - -
131H GLY* 5.6 0.3 - - - -
132H ALA* 4.0 18.6 + - - +
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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