Contacts of the helix formed by residues 109 - 119 (chain A) in PDB entry 5LUA
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 THR 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A MET* 3.8 2.1 - - - +
106A GLU 3.3 25.6 - - - +
107A ASP 3.1 7.3 + - - -
108A VAL* 1.3 74.8 - - - +
110A PRO* 1.3 75.2 - - - +
111A GLN* 3.6 12.1 + - - +
112A ASN* 3.0 31.8 + - - +
113A PHE* 3.0 23.4 + - - +
156A PHE* 3.5 6.5 - - - -
158A ASN* 6.1 3.6 - - + +
159A GLU* 5.5 1.6 - - + +
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Residues in contact with PRO 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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109A THR* 1.3 88.7 - - + +
111A GLN* 1.3 67.9 + - + +
113A PHE* 3.3 2.1 + - - +
114A LEU* 2.9 37.2 + - + +
156A PHE* 3.5 33.2 - - + -
159A GLU* 4.1 16.6 - - + -
160A ASP 3.6 28.5 - - - +
161A LEU* 3.9 24.0 - - + +
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Residues in contact with GLN 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 THR* 3.7 9.6 - - - +
110A PRO* 1.3 89.5 - - - +
112A ASN* 1.3 60.1 + - - +
114A LEU* 3.4 7.2 + - - +
115A ALA* 3.0 28.8 + - - +
118A ARG* 5.0 2.3 + - - -
159A GLU* 2.9 40.6 + - - +
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Residues in contact with ASN 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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69A MET* 4.1 8.1 - - + -
103A TYR* 4.6 6.0 - - + -
107A ASP* 2.7 36.8 + - - +
109A THR* 3.0 22.3 + - - +
111A GLN* 1.3 75.0 - - - +
113A PHE* 1.3 60.2 + - - +
115A ALA* 3.3 6.7 + - - +
116A VAL* 2.9 33.3 + - - +
123A ALA* 4.9 3.1 - - - +
124A VAL* 3.7 21.5 - - + +
127A ILE* 3.9 17.3 - - - +
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Residues in contact with PHE 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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32A VAL* 3.9 9.2 - - + -
34A VAL* 3.6 31.0 - - + -
69A MET* 3.7 16.5 - - - +
109A THR 3.0 14.9 + - - +
110A PRO 3.4 7.4 - - - +
112A ASN* 1.3 76.3 - - - +
114A LEU* 1.3 71.6 + - + +
116A VAL* 3.3 6.7 + - + +
117A LEU* 3.1 55.1 + - + +
143A ILE* 4.1 17.9 - - + -
145A PHE* 5.8 6.3 - + + -
154A LEU* 6.1 1.1 - - + -
156A PHE* 3.9 16.4 - + + -
161A LEU* 3.8 31.2 - - + -
166A LEU* 4.4 7.6 - - + -
184A PHE* 5.3 0.9 - + - -
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Residues in contact with LEU 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 PRO* 2.9 20.7 + - + +
111A GLN* 4.0 4.9 - - - +
113A PHE* 1.3 94.0 - - + +
115A ALA* 1.3 60.6 + - - +
117A LEU* 3.1 6.8 + - + +
118A ARG* 2.8 48.9 + - - +
161A LEU* 3.9 17.9 - - + -
165A ASP* 3.8 27.4 - - + +
166A LEU* 4.3 11.4 - - + -
169A THR* 3.4 31.6 - - + +
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Residues in contact with ALA 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 GLN 3.0 18.7 + - - +
112A ASN* 3.5 5.4 - - - +
114A LEU* 1.3 75.9 - - - +
116A VAL* 1.3 60.7 + - - +
118A ARG* 3.3 16.1 + - - +
119A GLY 3.1 3.5 + - - -
120A ASP* 2.8 33.6 + - + +
123A ALA* 3.8 28.5 - - + -
124A VAL* 4.0 12.8 - - + -
132A VAL* 4.1 3.3 - - - +
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Residues in contact with VAL 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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32A VAL* 4.0 22.2 - - + -
67A VAL* 3.9 31.6 - - + -
69A MET* 4.9 1.6 - - - -
103A TYR* 3.7 23.3 - - + +
112A ASN 2.9 19.6 + - - +
113A PHE* 3.3 13.0 + - - +
115A ALA* 1.3 75.3 - - - +
117A LEU* 1.3 62.1 + - + +
119A GLY* 3.2 5.2 + - - -
124A VAL* 5.4 0.7 - - + -
131A LYS 3.5 19.5 - - - +
132A VAL* 4.0 8.5 - - + +
133A LEU* 3.0 30.7 + - - +
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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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32A VAL* 4.1 17.9 - - + -
113A PHE* 3.1 55.2 + - + +
114A LEU* 3.1 12.2 + - + +
116A VAL* 1.3 77.2 - - + +
118A ARG* 1.3 58.1 + - - +
119A GLY 3.2 0.2 - - - -
133A LEU* 4.0 7.0 - - + +
143A ILE* 4.0 24.5 - - + -
166A LEU* 4.4 13.5 - - + -
169A THR* 3.8 21.1 - - + -
170A ILE* 5.6 0.7 - - + -
173A MET* 3.5 29.7 - - + +
178A MET* 3.1 20.4 - - - +
184A PHE* 4.9 2.2 - - + -
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Residues in contact with ARG 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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111A GLN 5.0 1.8 + - - -
114A LEU* 2.8 45.2 + - - +
115A ALA* 3.3 19.5 + - - +
117A LEU* 1.3 71.4 - - - +
119A GLY* 1.3 61.4 + - - +
120A ASP* 3.0 32.5 + - + +
123A ALA* 4.9 1.8 - - - +
169A THR* 3.8 20.4 + - + +
172A TYR* 3.7 50.0 + - + +
173A MET* 4.8 0.7 - - - -
178A MET* 3.5 21.0 - - - +
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Residues in contact with GLY 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 ALA 3.1 4.5 + - - -
116A VAL 3.2 2.3 + - - -
117A LEU 3.2 5.9 + - - -
118A ARG* 1.3 78.2 - - - +
120A ASP* 1.3 58.9 + - - +
121A ALA* 2.9 12.0 + - - +
132A VAL* 3.7 12.5 - - - +
133A LEU 3.1 26.9 - - - -
178A MET* 3.6 2.6 - - - +
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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