Contacts of the helix formed by residues 151 - 158 (chain W) in PDB entry 5L4K
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 GLU 151 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121W GLU* 4.4 2.9 - - - +
142W ASN* 4.3 8.5 + - - +
145W GLU 3.2 15.6 - - - +
146W GLU* 3.3 18.2 - - - +
149W ASN* 2.9 45.1 + - - +
150W THR* 1.3 75.3 - - - +
152W LYS* 1.3 63.3 + - - +
153W LEU* 3.8 4.9 - - + +
154W THR* 3.3 33.4 + - - +
170W LEU* 3.9 18.2 - - + -
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Residues in contact with LYS 152 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117W VAL* 3.3 35.5 + - + +
118W GLU 5.4 0.7 - - - -
119W ASP 3.1 31.0 - - - +
120W ASN* 4.5 4.3 - - - +
121W GLU* 3.4 42.5 - - + +
124W LEU* 4.3 15.4 - - + +
149W ASN* 3.8 10.9 + - - +
150W THR* 2.8 15.2 + - + +
151W GLU* 1.3 70.6 - - - +
153W LEU* 1.3 64.5 + - + +
154W THR 3.1 1.1 - - - -
155W ALA* 3.1 6.1 + - - +
156W PHE* 3.1 17.8 + - - +
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Residues in contact with LEU 153 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86W PHE* 4.0 39.0 - - + -
113W VAL* 4.7 5.8 - - + -
117W VAL* 5.2 9.9 - - + -
124W LEU* 5.0 8.5 - - + -
140W ILE* 4.1 16.8 - - + -
142W ASN* 3.8 23.6 - - - +
145W GLU* 4.8 5.8 - - - +
149W ASN* 4.4 17.5 - - - +
151W GLU* 3.0 4.2 - - + -
152W LYS* 1.3 79.6 - - + +
154W THR* 1.3 59.4 + - - +
156W PHE* 3.4 9.5 - - + +
157W VAL* 2.9 33.3 + - - +
170W LEU* 3.7 21.1 - - + -
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Residues in contact with THR 154 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151W GLU* 3.3 27.7 + - - +
152W LYS 3.1 0.6 - - - -
153W LEU* 1.3 76.7 - - - +
155W ALA* 1.3 57.5 + - - +
157W VAL* 3.3 6.2 + - + +
158W ASN* 3.0 51.3 + - - +
170W LEU* 3.7 12.7 - - - +
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Residues in contact with ALA 155 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121W GLU* 3.2 38.5 + - + +
125W VAL* 3.4 9.3 - - + +
151W GLU 4.5 0.2 + - - -
152W LYS 3.1 2.8 + - - -
154W THR* 1.3 78.1 - - - +
156W PHE* 1.3 54.1 + - - +
158W ASN* 4.1 7.9 - - - +
159W THR* 2.6 31.9 + - - -
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Residues in contact with PHE 156 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86W PHE* 4.1 26.5 - + - -
90W ILE* 4.9 8.1 - - + -
124W LEU* 3.3 46.4 - - + -
125W VAL* 4.6 3.8 - - - +
127W LEU* 4.6 6.1 - - + -
128W ALA* 3.9 20.3 - - + +
131W LEU* 4.4 17.9 - - + -
138W VAL* 3.8 25.1 - - + -
140W ILE* 4.1 16.8 - - + -
152W LYS 3.1 8.0 + - - +
153W LEU* 3.4 20.6 - - + +
154W THR 3.1 0.6 - - - -
155W ALA* 1.3 78.1 - - - +
157W VAL* 1.3 63.9 + - + +
159W THR* 3.4 16.2 + - - -
160W LEU* 3.7 13.5 + - + +
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Residues in contact with VAL 157 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138W VAL 5.0 0.4 - - - +
140W ILE* 3.9 21.1 - - + -
153W LEU 2.9 18.5 + - - +
154W THR* 3.4 14.4 - - + +
156W PHE* 1.3 77.3 - - + +
158W ASN* 1.3 70.5 + - - +
160W LEU 4.0 1.1 - - - -
161W ASN* 3.0 30.1 + - - +
168W SER* 3.3 31.7 - - - +
169W HIS* 4.1 3.4 - - - +
170W LEU* 3.8 37.0 - - + +
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Residues in contact with ASN 158 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154W THR* 3.0 37.7 + - - +
155W ALA* 4.6 5.6 - - - +
157W VAL* 1.3 84.4 - - - +
159W THR* 1.3 63.7 + - - +
160W LEU 3.2 2.0 - - - -
161W ASN* 3.3 29.9 + - - +
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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