Contacts of the helix formed by residues 109 - 123 (chain A) in PDB entry 4H7Y
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 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A ARG* 3.3 16.4 - - - +
104A GLU* 2.8 40.7 + - - +
105A LEU* 4.0 0.9 + - - -
107A GLN* 3.9 16.8 + - - +
108A GLY* 1.3 78.6 - - - +
110A VAL* 1.3 58.4 + - - +
111A LYS 3.4 2.2 - - - -
112A LYS* 3.3 12.2 + - + +
113A SER* 3.0 27.5 + - - -
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Residues in contact with VAL 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LEU* 3.8 22.2 - - + -
108A GLY* 3.2 15.5 + - - +
109A ASN* 1.3 73.1 - - - +
111A LYS* 1.3 64.8 + - + +
113A SER* 3.4 6.9 + - - -
114A LYS* 3.1 22.5 + - + +
138A LEU* 4.1 18.3 - - + +
141A GLN* 6.4 2.7 - - + -
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Residues in contact with LYS 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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109A ASN 3.4 0.4 - - - -
110A VAL* 1.3 77.8 - - + +
112A LYS* 1.3 61.0 + - - +
114A LYS* 3.3 7.6 + - - +
115A GLN* 2.9 43.1 + - + +
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Residues in contact with LYS 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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80A ARG* 6.5 0.4 - - - +
87A ARG* 5.6 3.6 - - - +
100A PHE* 5.5 4.0 - - - -
104A GLU* 3.8 27.1 - - + +
109A ASN* 3.3 22.3 + - + +
110A VAL 3.3 0.2 - - - -
111A LYS* 1.3 76.5 - - - +
113A SER* 1.3 66.0 + - - +
115A GLN* 3.2 33.5 + - - +
116A LEU* 2.9 49.2 + - + +
119A LYS* 5.3 8.3 - - - +
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Residues in contact with SER 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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101A ALA* 2.8 36.7 + - - +
104A GLU* 4.1 5.3 - - - +
105A LEU* 3.7 17.5 - - - +
109A ASN 3.0 17.2 + - - -
110A VAL* 3.6 7.6 - - - -
111A LYS 3.3 0.2 - - - -
112A LYS* 1.3 78.1 - - - +
114A LYS* 1.3 62.5 + - - +
116A LEU* 3.3 2.6 + - - +
117A LEU* 3.2 25.1 + - - +
138A LEU* 4.0 12.9 - - - +
145A LEU* 4.0 6.1 - - - +
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Residues in contact with LYS 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 VAL* 3.1 11.7 + - + +
111A LYS* 3.6 9.2 - - - +
113A SER* 1.3 74.9 - - - +
115A GLN* 1.3 65.6 + - - +
117A LEU* 3.2 4.2 + - - +
118A GLN* 3.0 59.9 + - + +
135A LEU* 4.4 9.6 - - + -
138A LEU* 3.5 23.5 - - + +
139A ASN* 5.1 10.7 + - - +
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Residues in contact with GLN 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 LYS* 2.9 39.9 + - + +
112A LYS* 3.3 37.9 + - - +
114A LYS* 1.3 75.8 - - - +
116A LEU* 1.3 64.7 + - - +
118A GLN* 3.3 9.9 + - - +
119A LYS* 2.9 42.7 + - - +
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Residues in contact with LEU 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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87A ARG* 3.3 34.6 + - - +
97A HIS* 4.5 12.6 + - + +
100A PHE* 3.7 32.3 - - + -
101A ALA* 3.9 17.7 - - + +
104A GLU* 3.6 30.1 - - + -
112A LYS* 2.9 40.5 + - + +
113A SER 3.7 4.0 - - - +
114A LYS 3.2 0.2 - - - -
115A GLN* 1.3 77.4 - - - +
117A LEU* 1.3 63.2 + - - +
119A LYS* 3.5 6.2 + - + +
120A ALA* 3.1 22.0 + - - +
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Residues in contact with LEU 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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97A HIS 4.6 1.1 - - - +
98A ILE* 3.6 33.2 - - + +
101A ALA* 3.7 16.2 - - + -
113A SER 3.2 14.5 + - - +
114A LYS 3.2 2.9 + - - +
116A LEU* 1.3 79.5 - - - +
118A GLN* 1.3 62.7 + - - +
120A ALA* 3.3 6.1 + - - +
121A VAL* 3.1 26.5 + - - +
131A LEU* 4.2 10.0 - - + +
134A ALA* 3.8 37.2 - - + +
135A LEU* 3.8 25.4 - - + +
138A LEU* 4.3 11.4 - - + -
145A LEU* 4.0 12.1 - - + -
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Residues in contact with GLN 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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114A LYS* 3.0 52.2 + - - +
115A GLN* 3.8 9.7 - - - +
117A LEU* 1.3 76.2 - - - +
119A LYS* 1.3 57.0 + - + +
121A VAL* 3.3 9.0 + - - +
122A GLU* 2.9 29.7 + - - +
135A LEU* 4.2 17.7 - - + +
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Residues in contact with LYS 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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87A ARG* 4.7 12.6 - - - +
97A HIS* 5.4 0.9 - - - +
112A LYS* 5.3 7.2 - - - +
115A GLN* 2.9 39.1 + - + +
116A LEU* 3.8 6.1 - - + +
118A GLN* 1.3 75.7 - - + +
120A ALA* 1.3 58.1 + - - +
122A GLU* 3.3 17.4 + - - +
123A ARG* 2.9 70.7 + - - +
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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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97A HIS* 3.5 49.5 + - + +
116A LEU 3.1 8.5 + - - +
117A LEU 3.5 9.2 - - - +
118A GLN 3.3 0.2 - - - -
119A LYS* 1.3 76.0 - - - +
121A VAL* 1.3 61.8 + - - +
123A ARG* 3.3 2.7 + - - -
124A GLY 3.0 4.5 + - - -
125A ALA* 2.9 27.6 + - + +
131A LEU* 3.7 19.0 - - + +
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Residues in contact with VAL 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 LEU 3.1 15.1 + - - +
118A GLN* 3.3 8.9 + - - +
120A ALA* 1.3 76.5 - - - +
122A GLU* 1.3 63.5 + - - +
124A GLY* 3.1 14.3 + - - -
125A ALA 5.0 0.4 - - - +
128A LEU* 4.0 21.9 - - + +
131A LEU* 3.8 29.6 - - + -
132A GLU* 5.7 1.3 - - + -
135A LEU* 4.0 17.7 - - + -
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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 GLN 2.9 17.6 + - - +
119A LYS* 3.7 19.9 + - - +
121A VAL* 1.3 79.4 - - - +
123A ARG* 1.3 69.3 + - - +
124A GLY* 3.6 0.5 + - - -
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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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87A ARG* 4.1 25.3 - - - +
91A LYS* 6.5 2.2 - - + -
97A HIS* 5.3 9.5 - - + -
119A LYS* 2.9 54.6 + - - +
120A ALA* 4.1 4.9 - - - +
121A VAL 3.1 0.4 - - - -
122A GLU* 1.3 88.8 + - + +
124A GLY* 1.3 63.0 + - - +
125A ALA* 3.4 2.2 - - + +
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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