Contacts of the helix formed by residues 218 - 226 (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 SER 218 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A VAL* 4.1 1.6 - - - -
150A GLY 3.5 10.3 - - - -
151A SER 3.5 1.8 + - - -
152A ALA* 3.7 23.0 - - - +
217A VAL* 1.3 77.2 - - - +
219A SER* 1.3 64.9 + - - +
220A GLU* 3.5 17.5 + - - +
221A GLN* 3.0 45.1 + - - +
222A VAL* 3.1 14.0 + - - +
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Residues in contact with SER 219 (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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101A ASP* 4.7 6.9 + - - -
149A VAL* 3.6 24.6 - - - +
150A GLY 4.4 1.6 + - - -
218A SER* 1.3 74.0 - - - +
220A GLU* 1.3 63.7 + - - +
222A VAL* 3.4 7.4 - - - +
223A LEU* 2.9 49.9 + - - +
226A ARG* 5.5 0.7 + - - -
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Residues in contact with GLU 220 (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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218A SER* 3.5 19.0 + - - +
219A SER* 1.3 85.6 + - - +
221A GLN* 1.3 61.6 + - + +
223A LEU* 3.5 12.5 + - + +
224A LYS* 3.2 37.0 + - - +
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Residues in contact with GLN 221 (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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152A ALA* 4.1 6.9 - - - +
153A LYS* 3.0 47.0 + - - +
154A PRO* 5.0 0.4 - - - +
156A LEU* 4.0 14.5 - - + +
157A GLN* 2.9 39.6 + - - +
160A VAL* 4.0 18.7 - - + +
217A VAL* 3.5 7.3 - - + +
218A SER* 3.0 32.0 + - - +
220A GLU* 1.3 77.3 - - + +
222A VAL* 1.3 62.1 + - - +
224A LYS* 3.2 13.2 + - - +
225A PHE* 3.4 18.0 + - - -
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Residues in contact with VAL 222 (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 TRP* 4.7 12.1 - - + -
101A ASP* 4.0 2.0 - - - +
115A ALA* 4.9 9.2 - - + +
116A ALA* 5.1 5.4 - - + -
147A LEU* 6.2 0.2 - - + -
149A VAL* 4.0 17.5 - - + -
217A VAL* 4.6 12.7 - - + +
218A SER 3.1 13.5 + - - +
219A SER* 3.4 12.1 - - - +
221A GLN* 1.3 75.2 - - - +
223A LEU* 1.3 68.7 + - + +
225A PHE* 3.0 32.4 + - + +
226A ARG* 3.2 47.3 + - - +
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Residues in contact with LEU 223 (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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219A SER* 2.9 40.1 + - - +
220A GLU* 3.7 13.7 - - + +
221A GLN 3.3 0.2 - - - -
222A VAL* 1.3 75.8 - - - +
224A LYS* 1.3 63.2 + - + +
226A ARG* 3.1 40.5 + - + +
227A LYS* 3.4 22.6 + - - +
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Residues in contact with LYS 224 (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* 4.6 6.1 - - - +
160A VAL* 3.4 35.0 - - + +
161A ASP* 4.4 12.8 + - - +
163A LEU* 4.0 13.7 - - + +
220A GLU* 3.2 20.4 + - - +
221A GLN 3.2 9.3 + - - +
222A VAL 3.1 0.8 - - - -
223A LEU* 1.3 75.9 - - + +
225A PHE* 1.3 63.9 + - - +
227A LYS* 3.2 38.7 + - + +
228A LEU* 3.9 3.8 + - - +
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Residues in contact with PHE 225 (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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66A PHE* 4.0 12.6 - + - -
95A PHE* 3.7 51.6 - + + -
97A TRP* 3.5 50.7 + + + +
116A ALA* 5.0 2.2 - - + -
147A LEU* 4.5 8.3 - - + -
156A LEU* 4.2 15.7 - - + -
159A VAL* 4.9 1.1 - - + -
160A VAL* 4.1 20.2 - - + -
163A LEU* 3.7 18.2 - - + -
221A GLN 3.4 9.6 + - - -
222A VAL* 3.0 19.4 + - + +
224A LYS* 1.3 75.6 - - - +
226A ARG* 1.3 56.3 + - - +
227A LYS 3.2 4.6 + - - -
228A LEU* 3.2 24.0 + - - +
240A MET 3.8 0.5 - - - +
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Residues in contact with ARG 226 (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 TRP* 4.0 6.1 - - + -
98A GLY 2.8 27.0 + - - +
99A SER* 3.7 22.6 + - - +
100A LEU* 3.4 19.1 + - - +
101A ASP* 2.8 30.7 + - - +
115A ALA* 5.1 4.2 + - - +
219A SER* 5.5 0.8 + - - -
222A VAL* 3.5 35.7 - - - +
223A LEU* 3.1 39.1 + - + +
225A PHE* 1.3 74.8 - - - +
227A LYS* 1.3 58.8 + - - +
228A LEU 3.4 1.9 - - - +
239A LEU* 3.6 28.7 - - + +
240A MET 4.0 8.3 - - - -
241A VAL* 3.8 11.0 - - + +
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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