Contacts of the helix formed by residues 220 - 225 (chain A) in PDB entry 2HCT
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 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A SER* 3.3 17.3 + - - -
127A ARG* 3.7 20.2 - - - +
217A ASP* 2.7 25.3 + - - +
219A ASP* 1.3 78.4 - - - +
221A THR* 1.3 65.9 + - - +
222A PHE* 3.6 2.8 + - - +
223A GLY 3.1 12.8 + - - -
224A SER* 2.8 25.9 + - - -
301A NMN 3.2 21.3 - - - -
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Residues in contact with THR 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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189A TRP* 4.5 9.0 - - - +
190A LYS* 5.2 0.8 + - - -
193A SER* 3.2 36.6 - - - +
220A SER* 1.3 70.2 - - - +
222A PHE* 1.3 64.9 + - - +
224A SER* 4.0 5.2 - - - -
225A VAL* 2.8 34.6 + - + +
226A GLY 3.0 7.1 + - - +
301A NMN 2.9 48.5 + - + +
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Residues in contact with PHE 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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124A LEU* 3.8 30.1 - - + -
125A TRP 4.2 6.5 - - - +
126A SER* 4.1 7.9 - - - +
206A VAL* 3.8 30.1 - - + -
208A LEU* 4.1 13.9 - - + -
216A PHE* 3.8 24.0 - + - -
220A SER* 3.2 4.7 - - - +
221A THR* 1.3 76.9 - - - +
223A GLY* 1.3 59.7 + - - +
226A GLY* 3.1 7.9 + - - +
227A VAL* 2.8 61.2 + - + +
230A LEU* 5.6 0.9 - - + -
238A LEU* 3.8 23.6 - - + -
262A LEU* 4.0 9.0 - - + -
301A NMN 3.2 19.9 + - - +
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Residues in contact with GLY 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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216A PHE* 3.7 28.9 - - - -
217A ASP 3.7 8.7 - - - -
218A LYS* 3.4 10.3 - - - +
220A SER* 3.1 12.5 + - - -
222A PHE* 1.3 78.1 - - - +
224A SER* 1.3 57.9 + - - +
227A VAL* 4.0 5.4 - - - +
228A HIS* 3.3 23.3 + - - -
265A ILE* 6.1 0.2 - - - +
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Residues in contact with SER 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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190A LYS* 5.8 1.1 - - - -
218A LYS 3.6 11.9 - - - -
219A ASP* 4.4 6.3 + - - -
220A SER 2.8 20.9 + - - -
221A THR* 4.0 1.4 - - - -
223A GLY* 1.3 77.4 - - - +
225A VAL* 1.3 72.4 + - - +
228A HIS* 3.7 18.9 - - - +
229A ASN* 5.1 0.5 + - - -
99B CYS* 5.7 1.6 - - - -
179B ASP 4.8 8.5 - - - +
180B CYS* 5.6 2.9 - - - +
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Residues in contact with VAL 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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190A LYS* 3.9 39.5 - - + +
193A SER* 4.2 4.3 - - - -
194A ARG* 3.6 43.3 - - + +
221A THR* 2.8 25.1 + - + +
224A SER* 1.3 91.1 - - - +
226A GLY* 1.3 64.4 + - - +
227A VAL 3.5 1.3 - - - -
228A HIS 3.5 1.0 + - - -
229A ASN* 2.7 35.7 + - - +
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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