Contacts of the helix formed by residues 118 - 138 (chain A) in PDB entry 4NLG
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 118 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A VAL* 3.0 21.3 + - - +
116A GLU 3.2 4.6 + - - +
117A GLY* 1.3 76.4 - - - +
119A PHE* 1.3 70.8 + - - +
120A GLU* 3.3 16.6 + - - +
121A ASN* 2.7 56.6 + - - +
122A GLY 3.3 0.7 + - - -
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Residues in contact with PHE 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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1A MET 4.9 0.4 - - - -
2A ILE* 3.9 31.3 - - + +
117A GLY 3.6 3.6 + - - -
118A ASN* 1.3 77.1 - - - +
120A GLU* 1.3 66.3 + - + +
122A GLY* 3.1 12.0 + - - -
123A ILE* 3.1 19.2 + - + +
145A VAL* 3.4 19.3 - - + +
146A ALA* 3.9 17.7 - - - -
147A PRO* 4.1 3.1 - - + -
166A VAL* 3.8 14.8 - - + -
167A ILE 3.1 26.9 - - - -
168A ARG* 3.7 28.9 - - + -
169A PRO* 3.8 24.5 - - + -
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Residues in contact with GLU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ASN* 3.3 13.3 + - - +
119A PHE* 1.3 75.7 - - + +
121A ASN* 1.3 65.9 + - - +
123A ILE* 3.0 17.9 + - - +
124A GLU* 3.0 22.7 + - - +
127A ARG* 5.5 1.4 + - - -
168A ARG* 2.7 44.7 + - - +
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Residues in contact with ASN 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A VAL* 3.0 32.6 + - + +
116A GLU* 4.7 9.5 + - - +
118A ASN* 2.7 39.3 + - - +
120A GLU* 1.3 74.4 - - - +
122A GLY* 1.3 57.8 + - - +
124A GLU* 3.3 8.9 + - - +
125A LEU* 3.0 26.2 + - - +
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Residues in contact with GLY 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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2A ILE* 5.0 4.9 - - - -
4A ILE* 3.8 4.9 - - - +
111A VAL* 4.6 8.1 - - - -
115A VAL* 3.3 22.1 - - - +
118A ASN 3.3 4.6 + - - -
119A PHE 3.1 8.2 + - - -
121A ASN* 1.3 76.3 - - - +
123A ILE* 1.3 60.7 + - - +
125A LEU* 3.1 4.7 + - - +
126A ALA* 2.8 29.3 + - - +
145A VAL* 4.5 6.5 - - - -
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Residues in contact with ILE 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 PHE* 3.1 16.3 + - + +
120A GLU* 3.0 36.8 + - - +
122A GLY* 1.3 74.9 - - - +
124A GLU* 1.3 62.3 + - - +
126A ALA* 3.1 11.6 + - - +
127A ARG* 3.0 49.8 + - - +
145A VAL* 4.3 10.7 - - + +
164A LEU* 4.6 9.4 - - + +
166A VAL* 3.4 41.3 - - + -
168A ARG* 3.9 10.3 - - - +
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Residues in contact with GLU 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 3.0 11.4 + - - +
121A ASN* 3.4 11.7 - - - +
123A ILE* 1.3 76.0 - - - +
125A LEU* 1.3 58.1 + - - +
127A ARG* 3.0 31.1 + - - +
128A LYS* 2.9 41.3 + - + +
131A GLN* 5.6 0.5 - - - +
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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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4A ILE* 3.9 6.3 - - + -
95A HIS* 3.7 38.4 - - + +
111A VAL* 3.6 37.5 - - + -
114A LYS* 4.6 8.3 - - + -
115A VAL* 4.0 11.4 - - + -
121A ASN 3.0 14.2 + - - +
122A GLY* 3.3 8.1 - - - +
124A GLU* 1.3 75.1 - - - +
126A ALA* 1.3 65.6 + - - +
128A LYS* 3.1 8.8 + - + +
129A ILE* 2.9 36.7 + - + +
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Residues in contact with ALA 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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4A ILE* 4.0 14.3 - - + +
122A GLY 2.8 15.2 + - - +
123A ILE 3.2 10.5 - - - +
125A LEU* 1.3 72.4 - - - +
127A ARG* 1.3 62.8 + - - +
129A ILE* 3.4 8.5 + - - +
130A LYS* 3.1 26.2 + - - +
143A VAL* 4.2 6.9 - - + +
145A VAL* 3.6 20.6 - - + -
164A LEU* 3.6 21.8 - - + -
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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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120A GLU* 5.5 2.2 + - - -
123A ILE* 3.0 33.7 + - - +
124A GLU* 3.0 33.2 + - - +
126A ALA* 1.3 76.6 - - - +
128A LYS* 1.3 62.6 + - - +
130A LYS* 3.1 10.0 + - + +
131A GLN* 3.0 37.5 + - + +
164A LEU* 3.6 31.5 - - + +
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Residues in contact with LYS 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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95A HIS* 3.7 20.3 - - + -
124A GLU* 2.9 22.6 + - - +
125A LEU* 3.6 14.6 - - + +
127A ARG* 1.3 75.7 - - - +
129A ILE* 1.3 56.8 - - - +
131A GLN* 3.3 18.9 + - + +
132A GLU* 2.9 50.4 + - + +
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Residues in contact with ILE 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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4A ILE* 4.3 15.0 - - + -
6A VAL* 4.7 9.9 - - + -
92A LEU* 3.6 22.7 - - + -
95A HIS* 4.0 40.6 - - + +
109A LEU* 4.0 18.8 - - + -
125A LEU* 2.9 31.2 + - + +
126A ALA* 3.5 6.7 - - - +
128A LYS* 1.3 74.9 - - - +
130A LYS* 1.3 67.5 + - - +
132A GLU* 3.2 7.4 + - - +
133A ILE* 3.1 31.7 + - + +
141A VAL* 5.6 0.2 - - + -
143A VAL* 5.0 5.4 - - + -
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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 ALA 3.1 14.1 + - - +
127A ARG* 3.1 10.8 + - + +
129A ILE* 1.3 76.6 - - - +
131A GLN* 1.3 65.4 + - + +
133A ILE* 3.4 1.9 + - - +
134A LEU* 3.1 24.5 + - - +
139A ILE 4.9 0.9 - - - +
140A THR* 6.1 0.3 - - - -
141A VAL* 2.4 46.7 + - + +
143A VAL* 3.8 28.5 - - + -
162A ASN* 2.8 29.3 + - - -
163A GLY 3.2 24.1 + - - +
164A LEU* 4.2 12.1 - - + -
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Residues in contact with GLN 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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124A GLU* 5.6 0.5 - - - +
127A ARG* 3.0 28.0 + - + +
128A LYS* 3.5 21.4 - - + +
130A LYS* 1.3 75.5 - - + +
132A GLU* 1.3 59.5 + - - +
134A LEU* 3.3 8.9 + - - +
135A GLU* 2.8 33.3 + - - +
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Residues in contact with GLU 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 LEU* 3.5 23.0 - - + +
94A LYS* 6.0 1.0 - - - +
95A HIS* 2.6 35.6 + - - -
128A LYS* 2.9 32.7 + - + +
129A ILE* 3.2 5.9 + - - +
131A GLN* 1.3 74.9 - - - +
133A ILE* 1.3 60.2 + - + +
135A GLU* 4.5 4.3 - - - -
136A LYS* 2.8 71.8 + - + +
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Residues in contact with ILE 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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6A VAL* 4.6 4.5 - - + -
88A ILE* 3.7 39.3 - - + -
91A LEU* 4.8 15.0 - - + -
92A LEU* 3.8 23.3 - - + -
129A ILE* 3.1 22.0 + - + +
130A LYS* 4.0 4.3 - - - +
132A GLU* 1.3 79.0 - - + +
134A LEU* 1.3 57.6 + - - +
137A GLU* 3.0 26.0 + - + +
138A LYS 3.3 4.3 + - - -
139A ILE* 3.5 28.0 + - + +
141A VAL* 4.2 23.3 - - + -
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Residues in contact with LEU 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 3.1 18.2 + - - +
131A GLN* 3.7 7.2 - - - +
133A ILE* 1.3 78.1 - - - +
135A GLU* 1.3 59.5 - - - +
138A LYS* 2.8 40.1 + - - +
139A ILE 3.5 12.9 + - - +
140A THR* 3.6 31.9 - - + -
162A ASN* 6.2 0.2 - - - +
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Residues in contact with GLU 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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131A GLN 2.8 19.5 + - - +
132A GLU* 3.8 4.9 - - - +
134A LEU* 1.3 82.8 - - - +
136A LYS* 1.3 66.1 + - + +
138A LYS* 3.6 23.8 + - - +
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Residues in contact with LYS 136 (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 LEU* 3.7 35.2 - - + +
132A GLU* 2.8 49.9 + - + +
135A GLU* 1.3 81.0 - - + +
137A GLU* 1.3 67.7 + - + +
138A LYS* 4.6 3.1 - - - +
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Residues in contact with GLU 137 (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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18A VAL* 3.9 10.8 - - - +
84A PHE* 3.6 11.5 - - - -
87A ARG* 2.4 56.0 + - + +
88A ILE* 4.0 21.5 - - + -
91A LEU* 4.4 9.8 - - + +
133A ILE 3.0 13.2 + - - +
136A LYS* 1.3 87.8 - - + +
138A LYS* 1.3 74.0 - - - +
139A ILE* 3.0 21.7 + - + +
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Residues in contact with LYS 138 (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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14A GLN* 4.0 4.9 - - - +
18A VAL* 3.4 30.3 - - + +
24A LYS* 6.0 0.5 + - - -
133A ILE 3.3 0.4 + - - -
134A LEU* 2.8 38.9 + - - +
135A GLU* 3.6 22.7 + - - +
136A LYS 4.6 2.7 - - - +
137A GLU* 1.3 80.5 - - - +
139A ILE* 1.3 58.0 + - - +
140A THR* 5.1 0.7 - - - +
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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