Contacts of the helix formed by residues 219 - 227 (chain A) in PDB entry 5TH4
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 219 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A VAL* 4.2 1.1 - - - -
151A GLY 3.5 9.9 - - - -
152A SER 3.3 1.8 + - - -
153A ALA* 3.7 22.5 - - - +
218A VAL* 1.3 75.9 - - - +
220A SER* 1.3 65.9 + - - +
221A GLU* 3.5 17.9 + - - +
222A GLN* 3.1 37.5 + - - +
223A VAL* 3.1 23.0 + - - +
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Residues in contact with SER 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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101A ASP* 5.0 5.2 - - - -
150A VAL* 3.6 24.9 - - - +
151A GLY 4.4 1.6 + - - -
219A SER* 1.3 73.1 - - - +
221A GLU* 1.4 70.2 + - - +
223A VAL* 3.3 7.7 + - - +
224A LEU* 2.9 44.7 + - - +
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Residues in contact with GLU 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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161A VAL* 5.6 0.2 - - - -
219A SER* 3.5 17.8 + - - +
220A SER* 1.4 82.6 + - - +
222A GLN* 1.4 65.5 + - + +
224A LEU* 3.4 13.0 + - + +
225A LYS* 3.1 38.7 + - - +
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Residues in contact with GLN 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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153A ALA* 4.0 7.1 - - - +
154A LYS* 3.0 47.2 + - - +
155A PRO* 5.0 0.4 - - - +
157A LEU* 4.0 14.5 - - + +
158A GLN* 2.9 37.8 + - - +
161A VAL* 4.0 18.3 - - + +
218A VAL* 3.5 7.3 - - + +
219A SER* 3.1 31.6 + - - +
221A GLU* 1.4 77.1 - - + +
223A VAL* 1.4 62.6 + - - +
225A LYS* 3.2 14.0 + - - +
226A PHE* 3.4 17.9 + - - -
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Residues in contact with VAL 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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97A TRP* 4.7 12.3 - - + -
101A ASP* 4.0 8.1 - - - +
115A ALA* 4.8 11.2 - - + +
116A ALA* 5.1 4.0 - - + -
148A LEU* 6.4 0.2 - - + -
150A VAL* 4.0 11.4 - - + -
218A VAL* 4.5 12.0 - - + +
219A SER 3.1 14.8 + - - +
220A SER* 3.3 12.3 - - - +
222A GLN* 1.4 74.4 - - - +
224A LEU* 1.3 68.3 + - + +
226A PHE* 3.0 32.6 + - + +
227A ARG* 3.2 47.4 + - + +
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Residues in contact with LEU 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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220A SER* 2.9 36.0 + - - +
221A GLU* 3.6 13.9 - - + +
223A VAL* 1.3 76.2 - - - +
225A LYS* 1.3 64.8 + - + +
227A ARG* 3.1 39.2 + - + +
228A LYS* 3.4 19.0 + - + +
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Residues in contact with LYS 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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158A GLN* 4.5 6.5 - - - +
161A VAL* 3.3 34.5 - - + +
162A ASP* 4.1 14.5 + - - +
164A LEU* 3.9 14.1 - - + +
221A GLU* 3.1 21.6 + - - +
222A GLN 3.2 9.1 + - - +
224A LEU* 1.3 75.3 - - + +
226A PHE* 1.4 63.7 + - - +
228A LYS* 3.2 30.3 + - + +
229A LEU* 4.0 3.6 + - - +
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Residues in contact with PHE 226 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A PHE* 4.0 12.8 - + - -
95A PHE* 3.8 50.5 - + + -
97A TRP* 3.5 50.1 + + + +
116A ALA* 4.9 2.5 - - + -
148A LEU* 4.4 8.5 - - + -
157A LEU* 4.2 17.5 - - + -
160A VAL* 4.8 1.3 - - + -
161A VAL* 4.2 19.1 - - + -
164A LEU* 3.7 19.7 - - + -
218A VAL* 6.5 0.2 - - + -
222A GLN 3.4 9.4 + - - -
223A VAL* 3.0 19.7 + - + +
225A LYS* 1.4 74.9 - - - +
227A ARG* 1.3 58.8 + - - +
228A LYS 3.1 4.6 + - - -
229A LEU* 3.2 24.0 + - - +
241A MET 3.7 0.7 - - - +
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Residues in contact with ARG 227 (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 6.7 - - + -
98A GLY 2.8 26.9 + - - +
99A SER* 3.6 22.1 + - - +
100A LEU* 3.3 20.1 + - - +
101A ASP* 2.9 29.9 + - - +
115A ALA* 5.1 3.2 + - - +
223A VAL* 3.5 35.7 - - - +
224A LEU* 3.1 38.5 + - + +
226A PHE* 1.3 80.4 - - - +
228A LYS* 1.3 59.0 + - - +
229A LEU 3.4 2.0 + - - +
240A LEU* 3.8 28.5 - - + +
241A MET 4.0 1.3 - - - -
242A VAL* 3.6 17.8 - - + +
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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