Contacts of the helix formed by residues 155 - 164 (chain A) in PDB entry 1U1L
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 155 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A ARG* 2.8 40.3 + - - -
105A LYS* 4.0 4.9 - - - +
130A LYS 5.9 0.6 - - - +
153A PHE* 3.4 5.4 - - - +
154A ASP* 1.3 82.9 - - + +
156A HIS* 1.3 72.4 + - - +
157A ASP* 2.9 17.0 + - - +
158A SER* 2.9 37.1 + - - +
159A VAL* 3.8 2.3 + - - +
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Residues in contact with HIS 156 (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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72A MET* 4.6 3.1 - - + -
75A ARG* 3.4 21.2 + - - -
85A GLU* 5.3 6.9 + - + +
86A PRO 4.4 16.8 + - - -
87A LYS* 5.0 7.9 - - + -
103A THR* 3.7 33.4 - - + +
104A VAL 3.5 25.5 - - - +
105A LYS* 4.1 14.2 - - + +
155A ASP* 1.3 80.0 + - - +
157A ASP* 1.3 69.6 + - + +
159A VAL* 3.3 6.0 + - - +
160A ASP* 2.9 43.7 + - - +
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Residues in contact with ASP 157 (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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72A MET* 3.4 24.6 - - - +
73A ASN* 5.5 1.2 - - - +
75A ARG* 3.6 13.9 + - - +
88A ARG* 2.8 50.7 + - - +
155A ASP* 2.9 22.5 + - - +
156A HIS* 1.3 83.5 + - + +
158A SER* 1.3 59.5 + - - +
160A ASP* 4.0 3.8 - - - +
161A LYS* 2.8 36.1 + - - +
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Residues in contact with SER 158 (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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128A TYR* 2.9 29.7 + - - +
129A GLY* 3.4 10.6 - - - -
130A LYS 4.6 0.3 + - - -
153A PHE* 3.7 25.4 - - - +
155A ASP* 2.9 25.2 + - - +
157A ASP* 1.3 79.2 - - - +
159A VAL* 1.3 61.6 + - - +
161A LYS* 3.4 6.7 + - - +
162A ILE* 3.1 29.3 + - - +
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Residues in contact with VAL 159 (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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104A VAL* 3.6 16.6 - - + +
105A LYS* 3.4 37.0 - - - +
107A ILE* 3.4 25.4 - - + -
153A PHE* 3.8 14.6 - - + -
155A ASP 3.8 2.0 + - - +
156A HIS 3.3 9.1 + - - +
158A SER* 1.3 77.2 - - - +
160A ASP* 1.3 57.4 + - - +
162A ILE* 3.1 10.2 + - - +
163A VAL* 2.9 28.0 + - + +
179A LYS* 4.0 27.6 - - + -
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Residues in contact with ASP 160 (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 LYS* 4.8 8.6 - - - +
88A ARG* 3.7 27.7 + - + +
90A VAL* 6.5 0.7 - - - -
102A LEU 4.5 1.6 - - - +
103A THR* 5.8 1.4 - - - -
104A VAL 5.3 1.4 + - - +
156A HIS* 2.9 39.4 + - - +
157A ASP* 3.2 6.6 + - - +
159A VAL* 1.3 77.0 - - - +
161A LYS* 1.3 62.5 + - - +
162A ILE 3.1 0.9 + - - -
163A VAL* 3.5 7.4 - - - +
164A ILE* 3.2 27.6 + - + +
179A LYS* 3.1 33.6 + - - -
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Residues in contact with LYS 161 (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 ASP* 4.3 8.2 - - - +
88A ARG* 3.4 39.2 - - - +
127A GLN 4.8 2.6 + - - -
128A TYR* 2.9 49.5 + - + +
157A ASP* 2.8 29.8 + - - +
158A SER* 3.6 7.2 - - - +
160A ASP* 1.3 72.4 - - - +
162A ILE* 1.3 58.3 + - - +
164A ILE* 3.2 24.4 - - + +
165A GLN* 3.5 14.7 - - - +
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Residues in contact with ILE 162 (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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107A ILE* 4.2 2.7 - - + -
125A PHE* 3.7 19.3 - - + -
128A TYR* 3.3 31.0 - - + -
153A PHE* 3.5 37.7 - - + -
158A SER 3.1 16.8 - - - +
159A VAL* 3.1 8.5 + - - +
160A ASP 3.1 0.6 - - - -
161A LYS* 1.3 75.3 - - - +
163A VAL* 1.3 66.8 + - + +
164A ILE 3.1 1.6 - - - -
165A GLN* 3.1 13.2 + - - +
168A HIS* 3.1 31.8 + - + -
177A VAL* 3.6 28.7 - - + -
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Residues in contact with VAL 163 (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 VAL* 6.1 4.0 - - + -
94A ASP* 4.9 6.4 - - - +
107A ILE* 4.4 0.4 - - + -
159A VAL* 2.9 29.1 + - + +
160A ASP* 3.5 13.9 - - + +
162A ILE* 1.3 73.5 - - - +
164A ILE* 1.3 65.5 + - + +
165A GLN 3.3 8.1 - - - +
168A HIS* 4.9 1.1 - - - -
177A VAL* 4.2 22.1 - - + +
178A ARG* 4.1 8.1 - - - -
179A LYS* 4.0 46.9 - - + +
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Residues in contact with ILE 164 (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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12A GLN* 5.9 1.6 - - + +
13A LEU* 3.8 35.4 - - + +
88A ARG* 4.1 28.9 - - + +
89A ALA 4.2 20.4 - - - +
90A VAL* 4.9 12.6 - - + -
94A ASP* 5.4 5.3 - - - +
160A ASP* 3.2 20.1 + - + +
161A LYS* 3.2 23.6 - - + +
163A VAL* 1.3 81.1 - - + +
165A GLN* 1.3 67.1 + - + +
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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