Contacts of the helix formed by residues 156 - 163 (chain A) in PDB entry 4Z1K
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 LEU 156 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A PHE* 3.7 28.7 - - + -
147A LEU* 4.8 3.6 - - + -
153A LYS* 3.0 18.6 + - + +
155A GLY* 1.3 76.5 - - - +
157A GLN* 1.3 63.9 + - - +
158A LYS 3.3 2.5 - - - -
159A VAL* 3.0 30.6 + - + +
160A VAL* 3.1 17.6 + - + +
183A LEU* 3.9 18.2 - - + +
215A ILE* 5.8 0.7 - - + -
217A VAL* 3.7 29.8 - - + -
221A GLN* 4.0 15.5 - - + +
225A PHE* 4.2 20.9 - - + -
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Residues in contact with GLN 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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153A LYS 3.7 1.8 + - - -
154A PRO* 3.1 17.2 + - + +
156A LEU* 1.3 77.5 - - - +
158A LYS* 1.3 58.2 + - - +
160A VAL* 3.1 18.3 + - - +
161A ASP* 2.9 64.4 + - - +
221A GLN* 2.9 33.8 + - - +
224A LYS* 4.6 7.7 - - - +
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Residues in contact with LYS 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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154A PRO 4.7 1.4 + - - -
155A GLY 4.8 1.2 + - - +
156A LEU 3.3 0.8 - - - -
157A GLN* 1.3 78.5 - - - +
159A VAL* 1.3 62.3 + - - +
161A ASP* 3.6 5.3 + - - +
162A VAL* 3.6 12.0 + - - +
175A PHE* 3.5 19.8 - - + -
178A PHE* 4.2 22.0 - - + -
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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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59A ILE* 4.3 7.0 - - + -
66A PHE* 3.4 38.8 - - + -
68A VAL* 4.7 0.9 - - + -
93A PHE* 4.3 12.3 - - + -
95A PHE* 4.7 0.9 - - + -
156A LEU* 3.0 26.1 + - + +
158A LYS* 1.3 75.5 - - - +
160A VAL* 1.3 67.9 + - - +
162A VAL* 3.1 21.2 + - - +
163A LEU* 3.4 7.3 - - + +
175A PHE* 3.8 18.6 - - + -
178A PHE* 3.7 29.6 - - + -
225A PHE* 4.9 1.1 - - + -
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Residues in contact with VAL 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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156A LEU* 3.1 26.4 + - + +
157A GLN* 3.1 26.3 + - - +
159A VAL* 1.3 76.5 - - - +
161A ASP* 1.3 63.7 + - - +
163A LEU* 3.2 25.7 + - - +
164A ASP* 4.6 1.6 + - - -
221A GLN* 4.0 31.9 - - + +
224A LYS* 3.4 41.1 - - + +
225A PHE* 4.1 10.5 - - + -
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Residues in contact with ASP 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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157A GLN* 2.9 49.2 + - - +
158A LYS* 4.2 5.7 - - - +
159A VAL 3.2 0.2 - - - -
160A VAL* 1.3 78.9 - - - +
162A VAL* 1.3 59.4 + - - +
163A LEU 3.3 0.6 + - - -
164A ASP* 4.4 11.3 + - - +
224A LYS* 4.4 10.1 + - - +
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Residues in contact with VAL 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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59A ILE* 3.5 32.1 - - + -
158A LYS 3.6 7.7 + - - +
159A VAL 3.1 19.3 + - - +
161A ASP* 1.3 75.7 - - - +
163A LEU* 1.3 64.6 + - - +
164A ASP 3.2 2.9 - - - -
165A SER* 2.7 39.4 + - - +
166A ILE* 3.7 3.5 + - - +
173A ALA* 4.2 15.5 - - + -
174A ASP 4.7 3.4 - - - +
175A PHE* 3.8 25.6 - - + -
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Residues in contact with LEU 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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59A ILE* 4.2 5.8 - - + -
66A PHE* 3.8 33.9 - - + -
159A VAL 3.4 15.0 - - - +
160A VAL* 3.2 20.5 + - - +
162A VAL* 1.3 78.4 - - - +
164A ASP* 1.3 63.3 + - - +
166A ILE* 3.0 29.6 + - + -
167A LYS* 3.4 10.6 + - - -
224A LYS* 4.0 18.6 - - + +
225A PHE* 3.7 34.8 - - + +
228A LEU* 3.7 19.6 - - + +
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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