Contacts of the helix formed by residues 104 - 116 (chain A) in PDB entry 3E8N
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A ILE* 1.3 99.3 - - + +
105A PRO* 1.3 73.4 - - + +
106A ALA* 4.2 9.0 - - + +
107A ILE* 3.0 27.6 - - + +
108A ARG* 3.3 4.9 + - - +
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Residues in contact with PRO 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ILE 3.7 1.1 - - - +
104A LYS* 1.3 89.1 - - + +
106A ALA* 1.3 58.1 + - + +
108A ARG* 3.0 45.2 - - + +
109A ASN* 2.5 26.8 + - - +
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Residues in contact with ALA 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A LYS* 3.3 8.6 - - + -
105A PRO* 1.3 82.7 - - + +
107A ILE* 1.3 65.4 + - + +
109A ASN* 3.2 26.5 + - - +
110A GLN* 3.4 6.2 + - - +
113A ARG* 5.2 1.0 + - - -
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Residues in contact with ILE 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ILE* 3.4 41.5 - - + -
104A LYS* 3.0 29.6 - - + +
106A ALA* 1.3 71.4 - - + +
108A ARG* 1.3 61.8 + - - +
109A ASN 3.0 1.6 - - - -
110A GLN* 2.8 28.9 + - - +
111A ILE* 3.0 14.7 + - + +
214A GLN* 3.3 25.1 - - + +
218A SER* 3.3 26.9 - - - +
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Residues in contact with ARG 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A LEU* 6.4 2.2 - - + -
103A ILE* 4.5 9.2 - - + +
104A LYS 3.3 8.8 + - - +
105A PRO* 3.0 40.8 + - + +
107A ILE* 1.3 82.1 - - - +
109A ASN* 1.3 87.6 + - - +
111A ILE* 3.2 10.4 + - + +
112A ILE* 2.9 37.9 + - + +
134A TYR* 3.3 65.2 - - + +
139A ILE* 5.0 4.9 - - + -
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Residues in contact with ASN 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A PRO* 2.5 28.4 + - - +
106A ALA* 3.2 14.1 + - - +
108A ARG* 1.3 106.5 + - - +
110A GLN* 1.3 57.5 + - - +
112A ILE* 3.6 7.2 + - - +
113A ARG* 3.0 42.9 + - - +
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Residues in contact with GLN 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ALA 3.4 5.1 + - - +
107A ILE* 2.8 14.9 + - - +
109A ASN* 1.3 78.0 - - - +
111A ILE* 1.3 55.3 + - - +
113A ARG* 3.1 27.2 + - - +
114A GLU* 2.8 66.7 + - + +
214A GLN* 3.5 31.5 + - + +
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Residues in contact with ILE 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A LEU* 3.9 26.7 - - + -
103A ILE* 5.4 0.4 - - + -
107A ILE* 3.0 18.3 + - + +
108A ARG* 3.5 12.8 - - + +
110A GLN* 1.3 75.9 - - - +
112A ILE* 1.3 66.8 + - + +
114A GLU* 2.9 4.4 + - - +
115A LEU* 2.8 39.1 + - + +
139A ILE* 4.2 11.4 - - + -
212A SER* 4.1 11.2 + - - +
214A GLN* 3.5 29.6 - - + -
215A LEU* 3.6 33.0 - - + +
218A SER* 4.3 4.5 - - - +
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Residues in contact with ILE 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ARG* 2.9 24.3 + - - +
109A ASN* 3.9 7.0 - - - +
111A ILE* 1.3 78.0 - - + +
113A ARG* 1.3 63.3 + - - +
115A LEU* 3.4 12.8 + - + +
116A GLN* 2.9 37.7 + - + +
132A ALA* 4.3 6.1 - - - +
133A PHE* 4.0 9.4 - - - +
134A TYR* 3.9 32.1 - - + +
139A ILE* 3.5 36.8 - - + -
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Residues in contact with ARG 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ALA 5.2 1.0 + - - -
109A ASN* 3.0 33.6 + - - +
110A GLN* 3.1 39.3 + - - +
111A ILE 3.1 0.2 - - - -
112A ILE* 1.3 79.8 - - + +
114A GLU* 1.3 64.9 + - + +
116A GLN* 3.4 22.6 - - + +
117A VAL* 4.6 2.9 + - - +
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Residues in contact with GLU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A GLN* 2.8 48.5 + - + +
111A ILE 2.9 0.9 + - - +
113A ARG* 1.3 73.4 - - + +
115A LEU* 1.3 65.4 + - - +
116A GLN 3.1 0.4 - - - -
117A VAL* 3.1 24.0 - - + +
211A VAL* 3.7 11.3 - - - +
212A SER* 2.5 40.0 + - - -
213A GLY* 3.9 8.3 + - - -
214A GLN* 2.9 23.7 + - - +
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Residues in contact with LEU 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ILE* 2.8 23.1 + - + +
112A ILE* 3.8 8.7 - - + +
113A ARG 3.3 0.2 - - - -
114A GLU* 1.3 75.5 - - - +
116A GLN* 1.3 59.9 + - - +
117A VAL 3.2 0.4 - - - -
118A LEU* 2.9 38.5 + - + +
129A PHE* 4.0 2.4 - - - -
132A ALA* 3.7 30.1 - - + -
139A ILE* 3.4 32.1 - - + -
141A ILE* 3.9 11.0 - - + -
211A VAL* 4.1 3.8 - - + -
212A SER* 4.0 6.5 - - - -
215A LEU* 4.2 4.3 - - + -
1001A VRA 3.3 41.1 - - - -
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Residues in contact with GLN 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A ILE* 2.9 30.0 + - + +
113A ARG* 3.4 18.8 - - + +
114A GLU 3.1 0.6 - - - -
115A LEU* 1.3 72.7 - - - +
117A VAL* 1.3 59.7 + - + +
118A LEU* 2.8 11.7 + - - -
119A HIS* 2.9 47.9 + - - +
120A GLU* 4.3 2.1 - - - +
129A PHE* 5.1 1.6 - - - -
132A ALA* 3.3 33.6 + - - +
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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