Contacts of the helix formed by residues 121 - 135 (chain A) in PDB entry 2X5N
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 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A VAL 3.7 2.0 + - - -
120A GLU* 1.3 75.8 - - - +
122A GLU* 1.3 60.8 + - - +
123A LYS* 3.5 7.4 + - - +
124A ASN* 3.0 38.3 + - - +
125A LEU* 2.9 26.2 + - - +
1195A SO4 3.4 25.4 + - - +
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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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121A ASP* 1.3 69.4 - - - +
123A LYS* 1.3 67.3 + - - +
125A LEU* 3.0 11.1 + - + +
126A ILE* 2.9 35.0 + - + +
152A ALA* 4.0 23.8 - - + +
155A HIS* 2.5 43.5 + - - +
1195A SO4 2.7 26.6 + - - +
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Residues in contact with LYS 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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121A ASP* 3.4 9.1 + - - +
122A GLU* 1.3 77.8 - - - +
124A ASN* 1.3 63.1 + - - +
126A ILE* 3.3 6.8 + - - +
127A ARG* 3.1 63.9 + - + +
1195A SO4 5.0 1.6 + - - +
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Residues in contact with ASN 124 (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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120A GLU* 4.3 17.5 - - + -
121A ASP* 3.0 37.4 + - - +
123A LYS* 1.3 77.5 - - - +
125A LEU* 1.3 59.3 + - - +
127A ARG* 3.4 33.2 + - - +
128A LEU* 2.9 35.3 + - + +
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Residues in contact with LEU 125 (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 PHE* 3.6 36.1 - - + -
118A ILE* 3.9 31.2 - - + -
120A GLU* 4.3 5.5 - - + +
121A ASP 2.9 18.6 + - - +
122A GLU* 3.0 13.2 + - + +
124A ASN* 1.3 72.9 - - - +
126A ILE* 1.3 59.5 + - + +
128A LEU* 3.3 10.4 + - + +
129A ALA 3.0 22.5 + - - -
152A ALA* 4.0 34.8 - - + +
153A LEU* 4.6 2.7 - - + -
156A PHE* 3.2 29.6 - - + -
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Residues in contact with ILE 126 (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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122A GLU* 2.9 31.3 + - + +
123A LYS* 3.8 6.3 - - - +
124A ASN 3.2 0.2 - - - -
125A LEU* 1.3 74.4 - - + +
127A ARG* 1.3 67.3 + - - +
129A ALA* 3.2 3.6 + - - +
130A LYS* 2.9 50.2 + - + +
152A ALA 5.2 0.4 - - - +
155A HIS* 3.6 42.4 - - + +
156A PHE* 3.9 7.6 - - + +
159A ALA* 4.2 7.6 - - + -
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Residues in contact with ARG 127 (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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123A LYS* 3.1 50.2 + - + +
124A ASN* 3.4 33.5 + - - +
126A ILE* 1.3 77.3 - - + +
128A LEU* 1.3 62.5 + - + +
130A LYS* 4.0 5.1 - - - +
131A ARG* 3.0 25.3 + - - +
1196A SO4 3.3 35.4 + - - +
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Residues in contact with LEU 128 (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 PHE* 4.8 4.0 - - + -
88A GLY* 3.8 26.9 - - - +
91A ILE* 4.6 10.8 - - + -
92A GLN* 3.7 38.1 - - + +
95A GLN* 5.2 1.8 + - - +
120A GLU* 3.8 18.6 - - + -
124A ASN* 2.9 22.2 + - + +
125A LEU* 3.4 21.5 - - + +
126A ILE 3.2 0.2 - - - -
127A ARG* 1.3 76.4 - - + +
129A ALA* 1.3 55.9 + - - +
131A ARG* 3.4 5.5 + - - +
132A MET* 3.0 31.7 + - - +
156A PHE* 4.1 8.7 - - + -
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Residues in contact with ALA 129 (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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125A LEU 3.0 12.9 + - - +
126A ILE 3.2 8.0 + - - +
128A LEU* 1.3 77.4 - - - +
130A LYS* 1.3 57.5 + - - +
132A MET* 3.2 6.6 + - - +
133A LYS 3.0 23.0 + - - -
156A PHE* 3.3 41.9 - - + +
159A ALA* 3.7 12.3 - - + -
160A ALA* 3.6 18.3 - - + +
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Residues in contact with LYS 130 (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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126A ILE* 2.9 39.5 + - + +
127A ARG* 4.1 4.5 - - - +
129A ALA* 1.3 76.3 - - - +
131A ARG* 1.3 57.2 + - - +
133A LYS* 3.3 5.4 + - + +
134A LYS* 2.9 28.2 + - - +
159A ALA* 4.2 23.1 - - + +
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Residues in contact with ARG 131 (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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95A GLN* 5.0 4.9 - - - +
127A ARG 3.0 19.1 + - - +
128A LEU* 3.6 6.5 - - - +
130A LYS* 1.3 74.0 - - - +
132A MET* 1.3 59.9 + - - +
134A LYS* 3.2 34.6 + - - +
135A ASN* 2.9 55.1 + - - +
1196A SO4 2.8 43.7 + - - +
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Residues in contact with MET 132 (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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91A ILE* 3.8 19.3 - - + -
95A GLN* 3.6 25.6 - - - +
110A ILE* 3.6 15.7 - - + -
128A LEU 3.0 18.1 + - - +
129A ALA* 3.2 8.3 + - - +
131A ARG* 1.3 74.1 - - - +
133A LYS* 1.3 64.4 + - - +
135A ASN* 3.0 2.6 + - - -
136A ASN 3.0 18.4 + - - -
137A VAL* 3.0 58.0 + - + +
138A ALA 3.7 9.0 - - - +
139A ILE* 3.7 27.4 - - + -
156A PHE* 4.4 7.6 - - - -
160A ALA* 4.9 3.4 - - + -
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Residues in contact with LYS 133 (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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129A ALA 3.0 12.0 + - - +
130A LYS* 3.6 9.9 - - + +
132A MET* 1.3 76.0 - - - +
134A LYS* 1.3 63.3 + - - +
136A ASN* 3.1 20.9 + - - +
137A VAL 4.8 2.0 - - - -
158A ASP 5.8 1.0 + - - -
159A ALA 3.5 19.5 + - - +
160A ALA 3.5 19.5 + - - +
161A ASN 3.4 21.6 + - - +
162A SER* 4.3 17.6 - - - +
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Residues in contact with LYS 134 (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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130A LYS 2.9 16.8 + - - +
131A ARG* 3.5 37.9 - - - +
133A LYS* 1.3 77.5 - - - +
135A ASN* 1.3 63.2 + - - +
136A ASN* 3.3 9.2 + - - -
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Residues in contact with ASN 135 (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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95A GLN* 3.0 26.5 + - - +
99A LYS* 6.3 1.7 - - - +
108A GLN* 4.1 9.9 + - - -
131A ARG* 2.9 43.0 + - - +
132A MET 3.0 4.9 + - - +
134A LYS* 1.3 82.4 - - - +
136A ASN* 1.3 68.3 + - - +
137A VAL* 3.3 11.7 + - + +
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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