Contacts of the helix formed by residues 107 - 123 (chain A) in PDB entry 4HNE
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 107 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A PHE* 2.9 13.8 + - + +
106A GLU* 1.3 82.3 - - - +
108A PRO* 1.4 64.5 - - - +
109A GLU* 3.0 6.8 + - - +
110A PHE* 3.0 28.8 + - + +
111A GLU 3.2 8.3 + - - -
201A GLN* 5.3 0.2 - - - +
210A ARG* 2.6 52.5 + - - +
212A LYS* 4.1 17.9 - - - +
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Residues in contact with PRO 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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104A PHE 3.5 5.4 - - - +
105A PRO* 3.7 13.2 - - + +
106A GLU 3.6 7.9 - - - +
107A ASP* 1.4 87.5 - - - +
109A GLU* 1.3 62.7 + - + +
111A GLU* 3.4 8.7 + - + +
112A ALA* 3.1 22.7 + - - +
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Residues in contact with GLU 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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107A ASP* 3.0 10.2 + - - +
108A PRO* 1.3 80.3 - - + +
110A PHE* 1.3 60.9 + - - +
112A ALA* 3.5 8.5 + - + +
113A VAL* 3.3 25.8 + - + +
210A ARG* 3.7 19.1 + - - +
262A LEU* 6.1 1.5 - - + +
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Residues in contact with PHE 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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104A PHE* 4.0 13.0 - + - -
107A ASP* 3.0 27.2 + - + +
109A GLU* 1.3 76.5 - - - +
111A GLU* 1.3 64.8 + - - +
113A VAL* 3.1 18.7 + - - +
114A VAL* 3.2 27.9 + - + +
210A ARG* 3.6 31.3 - - + +
212A LYS* 3.7 39.9 - - + -
214A VAL* 3.9 8.5 - - + -
260A PHE* 3.2 44.9 - + + -
262A LEU* 4.0 20.6 - - + -
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Residues in contact with GLU 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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102A ASN 3.7 10.3 - - - +
103A GLU* 3.9 10.2 - - - +
104A PHE* 2.5 50.9 + - + +
105A PRO* 3.9 1.0 - - - +
107A ASP 3.2 8.4 + - - +
108A PRO* 3.6 11.1 - - + +
109A GLU 3.3 0.2 - - - -
110A PHE* 1.3 79.1 - - - +
112A ALA* 1.3 63.2 + - - +
114A VAL* 3.1 8.2 + - - +
115A ARG* 2.9 55.6 + - + +
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Residues in contact with ALA 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 PRO 3.1 12.8 + - - +
109A GLU* 3.6 12.1 - - - +
110A PHE 3.2 0.2 - - - -
111A GLU* 1.3 73.8 - - - +
113A VAL* 1.3 65.7 + - + +
115A ARG* 3.1 12.8 + - - +
116A GLN* 3.0 25.7 + - - +
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Residues in contact with VAL 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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109A GLU* 3.3 19.5 - - + +
110A PHE* 3.1 9.1 + - - +
112A ALA* 1.3 77.0 - - + +
114A VAL* 1.3 61.6 + - - +
116A GLN* 3.2 11.1 + - - +
117A ALA* 3.0 18.0 + - - +
148A ILE* 3.5 34.8 - - + +
260A PHE* 4.1 7.4 - - + -
262A LEU* 3.7 35.2 - - + -
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Residues in contact with VAL 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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102A ASN* 3.8 34.5 - - + +
104A PHE* 4.5 3.8 - - + -
110A PHE* 3.4 37.7 - - + +
111A GLU* 3.1 10.7 + - - +
113A VAL* 1.3 77.2 - - - +
115A ARG* 1.3 58.9 + - - +
117A ALA* 3.0 4.5 + - - +
118A GLU* 2.9 37.0 + - + +
214A VAL* 4.3 12.8 - - + -
216A LEU* 5.0 3.8 - - + -
260A PHE* 3.9 21.5 - - + -
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Residues in contact with ARG 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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101A ARG* 2.7 30.5 + - - +
102A ASN* 3.3 11.4 + - - +
103A GLU* 5.3 1.6 - - - +
111A GLU* 2.9 54.9 + - + +
112A ALA* 3.1 9.6 + - - +
114A VAL* 1.3 73.0 - - - +
116A GLN* 1.3 56.2 + - - +
118A GLU* 2.8 41.2 + - - +
119A LEU* 2.7 38.5 + - - +
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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 ALA* 3.0 16.3 + - + +
113A VAL* 3.3 12.6 - - + +
115A ARG* 1.3 75.7 - - - +
117A ALA* 1.3 58.1 + - - +
119A LEU* 4.3 5.6 - - - +
120A ALA* 3.0 25.6 + - - +
142A ASP* 3.7 11.7 + - + +
143A PRO* 3.4 40.0 - - + +
144A GLN* 3.8 13.4 - - - +
146A ARG* 4.6 4.0 - - - +
148A ILE* 4.1 13.0 - - + +
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Residues in contact with ALA 117 (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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113A VAL 3.0 12.6 + - - +
114A VAL 3.2 9.4 - - - +
116A GLN* 1.3 73.0 - - - +
118A GLU* 1.3 64.8 + - - +
120A ALA* 3.7 2.4 + - - +
121A ILE* 3.1 31.4 + - - +
140A VAL* 3.5 27.2 - - + +
141A LYS 4.2 6.4 - - - +
148A ILE* 3.9 6.9 - - + +
216A LEU* 4.6 6.7 - - + -
260A PHE* 3.9 16.2 - - + -
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Residues in contact with GLU 118 (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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100A GLU 4.8 4.0 - - - +
101A ARG 5.2 0.2 - - - -
102A ASN* 3.3 23.2 + - - -
114A VAL* 2.9 18.9 + - - +
115A ARG* 2.8 46.2 + - - +
117A ALA* 1.3 74.0 - - - +
119A LEU* 1.3 65.3 + - - +
121A ILE* 3.3 10.9 + - - +
122A GLU* 3.1 34.1 + - + +
215A TYR 4.8 0.3 - - - +
216A LEU* 4.1 16.6 - - + -
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Residues in contact with LEU 119 (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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115A ARG 2.7 20.4 + - - +
116A GLN* 3.6 9.4 - - - +
118A GLU* 1.3 73.1 - - - +
120A ALA* 1.3 63.0 + - - +
122A GLU* 3.0 29.1 + - + +
123A ARG* 2.9 63.8 + - + +
143A PRO* 3.9 13.0 - - + -
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Residues in contact with ALA 120 (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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116A GLN 3.0 10.3 + - - +
117A ALA 3.8 3.6 - - - +
119A LEU* 1.3 75.1 - - - +
121A ILE* 1.3 53.4 + - + +
123A ARG* 3.4 5.1 + - - +
124A CYS 3.1 6.6 + - - -
125A ILE* 2.7 42.7 + - + +
141A LYS 3.1 28.0 - - - +
142A ASP 3.4 22.0 - - - +
143A PRO* 3.8 11.5 - - + +
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Residues in contact with ILE 121 (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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117A ALA* 3.1 17.5 + - + +
118A GLU* 3.3 8.2 + - - +
119A LEU 3.1 0.8 - - - -
120A ALA* 1.3 74.1 - - - +
122A GLU* 1.3 62.1 + - + +
124A CYS* 2.9 20.3 + - - +
125A ILE 3.9 5.8 - - - +
126A PHE* 3.8 23.7 - - + -
127A PRO* 3.9 33.9 - - + -
140A VAL* 5.5 0.7 - - + -
141A LYS 6.0 0.2 - - - +
216A LEU* 4.2 24.7 - - + -
217A ALA 3.5 28.0 - - - +
218A SER* 4.3 4.9 - - - -
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Residues in contact with GLU 122 (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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118A GLU* 3.1 22.0 + - - +
119A LEU* 3.0 30.7 + - + +
121A ILE* 1.3 76.9 - - + +
123A ARG* 1.3 59.7 + - + +
124A CYS* 3.2 11.4 + - - -
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Residues in contact with ARG 123 (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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119A LEU* 2.9 40.1 + - + +
120A ALA 3.8 0.4 - - - +
121A ILE 3.2 0.2 - - - -
122A GLU* 1.3 75.8 - - + +
124A CYS* 1.3 68.7 + - - +
125A ILE* 3.2 25.1 + - + +
143A PRO* 3.7 25.6 + - - +
144A GLN* 4.7 4.2 + - - -
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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