Contacts of the helix formed by residues 116 - 127 (chain A) in PDB entry 1LAN
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 ALA 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A PRO* 3.3 27.8 + - + +
114A GLY 4.2 0.2 - - - -
115A ASP* 1.3 70.7 + - - +
117A GLN* 1.3 60.4 + - - +
119A ALA* 4.3 1.1 - - - -
120A ALA* 2.9 30.8 + - - +
145A LEU* 4.7 1.3 - - + -
149A GLU 5.8 0.2 - - - +
150A ASP* 3.9 14.6 + - + +
153A ALA* 3.9 10.7 - - + +
154A TRP* 3.7 32.5 - - + +
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Residues in contact with GLN 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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86A LYS* 6.1 0.6 - - - +
115A ASP* 3.3 8.9 + - - +
116A ALA* 1.3 76.4 - - - +
118A ALA* 1.3 58.5 + - - +
120A ALA 3.3 1.4 + - - -
121A GLU* 2.9 51.7 + - - +
153A ALA* 3.3 22.3 + - + +
156A ARG* 3.1 40.2 - - - +
157A GLY* 3.4 22.4 - - - +
160A PHE* 4.1 15.6 - - - -
392A GLU* 5.2 9.9 + - - +
477A GLU* 5.2 1.6 - - - +
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Residues in contact with ALA 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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86A LYS* 3.9 27.4 - - + +
89A ILE* 3.8 15.3 - - + -
90A ARG* 3.5 14.1 - - + +
115A ASP* 3.2 25.4 + - - +
117A GLN* 1.3 76.9 - - - +
119A ALA* 1.3 64.4 + - - +
121A GLU* 3.2 13.1 + - - +
122A GLY 2.9 19.4 + - - -
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Residues in contact with ALA 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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89A ILE* 3.5 14.9 - - + +
93A VAL* 3.3 19.0 - - + +
110A VAL* 4.5 0.7 - - + -
111A ASP 3.7 22.9 - - - +
112A PRO* 3.7 18.2 - - + +
115A ASP 3.1 6.0 + - - +
116A ALA 3.8 5.6 - - - +
118A ALA* 1.3 75.1 - - - +
120A ALA* 1.3 62.6 + - - +
122A GLY 3.2 1.6 + - - -
123A ALA* 3.1 20.3 + - - +
154A TRP* 4.1 11.4 - - + -
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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 ALA 2.9 15.7 + - - +
117A GLN 3.5 5.2 - - - +
119A ALA* 1.3 78.1 - - - +
121A GLU* 1.3 56.7 + - - +
123A ALA* 3.3 0.7 + - - +
124A VAL* 3.0 34.8 + - - +
154A TRP* 3.2 54.4 - - + +
157A GLY 4.5 1.8 - - - -
158A VAL* 3.8 10.8 - - + +
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Residues in contact with GLU 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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90A ARG* 2.9 40.1 + - + +
117A GLN* 2.9 44.8 + - - +
118A ALA* 3.2 8.4 + - - +
120A ALA* 1.3 75.8 - - - +
122A GLY* 1.3 58.1 + - - +
125A LEU* 2.9 44.9 + - + +
157A GLY* 3.4 15.7 - - - +
160A PHE* 3.5 20.1 - - - +
161A ALA* 4.1 11.9 - - + -
473A ARG* 3.9 14.2 + - - -
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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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90A ARG* 3.3 32.9 - - - +
93A VAL* 4.5 0.7 - - - -
94A ALA* 3.4 14.6 - - - +
118A ALA 2.9 11.5 + - - -
119A ALA 3.2 3.8 + - - -
121A GLU* 1.3 77.4 - - - +
123A ALA* 1.3 55.6 + - - +
126A GLY* 2.8 29.6 + - - -
462A TYR* 4.6 3.8 - - - -
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Residues in contact with ALA 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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93A VAL* 3.6 9.7 - - + +
97A CYS* 3.7 25.4 - - - -
110A VAL* 4.4 0.9 - - + -
119A ALA 3.1 15.0 + - - +
120A ALA 3.8 3.4 - - - +
122A GLY* 1.3 76.2 - - - +
124A VAL* 1.3 59.7 + - + +
127A LEU* 3.0 38.0 + - - +
143A ALA* 4.2 17.5 - - + -
154A TRP* 4.4 11.7 - - + -
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Residues in contact with VAL 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 ALA* 3.0 19.3 + - - +
123A ALA* 1.3 76.5 - - + +
125A LEU* 1.3 64.2 + - - +
127A LEU* 4.4 2.3 - - - +
128A TYR 3.5 11.4 + - - -
143A ALA* 5.7 6.1 - - + +
154A TRP* 5.7 1.8 - - + -
158A VAL* 4.2 28.3 - - + +
161A ALA* 3.4 27.4 - - + -
162A SER* 4.1 11.4 - - - +
165A ASN* 3.1 29.3 + - - +
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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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121A GLU* 2.9 30.4 + - + +
122A GLY 4.5 0.2 - - - +
124A VAL* 1.3 72.8 - - - +
126A GLY* 1.3 63.0 + - - +
128A TYR* 3.5 6.4 + - - +
161A ALA* 3.7 23.3 - - + +
164A GLN* 3.7 28.3 - - + +
165A ASN* 3.5 17.5 - - - +
168A ARG* 3.2 22.5 + - - +
462A TYR* 3.3 43.3 - - + +
463A LEU* 4.1 7.8 - - + -
464A ARG 5.0 0.2 + - - -
473A ARG* 3.8 23.1 - - - +
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Residues in contact with GLY 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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94A ALA* 3.8 14.1 - - - -
97A CYS* 5.8 0.4 - - - -
98A ARG* 3.9 18.5 + - - +
122A GLY 2.8 21.8 + - - -
123A ALA 3.9 0.2 - - - -
125A LEU* 1.3 80.6 - - - +
127A LEU* 1.3 59.1 + - - +
128A TYR 3.6 0.2 + - - -
462A TYR 3.3 14.6 + - - -
464A ARG* 3.7 19.1 + - - +
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Residues in contact with LEU 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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97A CYS* 3.7 41.7 - - + +
98A ARG* 4.3 2.0 - - - +
101A GLN* 3.8 32.1 + - + +
123A ALA 3.0 21.8 + - - +
124A VAL* 4.6 2.0 - - - +
126A GLY* 1.3 75.6 - - - +
128A TYR* 1.3 65.2 + - - +
129A GLU* 3.6 3.5 + - - +
141A VAL* 3.8 40.8 - - + +
143A ALA* 4.3 15.7 - - + -
464A ARG* 3.0 14.8 + - - +
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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