Contacts of the helix formed by residues 217 - 222 (chain A) in PDB entry 3M4D
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 217 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A ASP* 3.6 25.8 + - - +
153A PHE* 3.5 23.2 - - - -
171A PHE* 5.8 0.4 - - - -
174A MET* 3.5 11.6 - - - +
213A PRO 4.7 0.5 - - - +
216A ALA* 1.3 74.4 - - - +
218A SER* 1.3 64.8 + - - +
219A LEU* 3.5 15.8 + - - +
220A LEU* 2.9 35.8 + - - +
221A SER* 4.1 2.9 + - - -
107G ILE* 5.6 0.2 - - - -
108G ASP* 4.3 9.8 + - - -
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Residues in contact with SER 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A PRO 5.3 1.1 - - - -
216A ALA 3.2 6.5 + - - -
217A SER* 1.3 71.8 + - - +
219A LEU* 1.3 64.2 + - - +
220A LEU 3.2 0.4 + - - -
221A SER* 3.3 6.6 + - - -
222A SER* 3.0 29.1 + - - -
223A GLY 3.2 4.2 + - - -
105G ASN* 3.5 33.2 + - - +
106G SER 4.0 7.6 + - - -
108G ASP* 4.5 5.3 + - - -
154G LYS* 5.1 6.5 - - - +
156G ILE* 4.3 26.2 - - - -
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Residues in contact with LEU 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLY* 3.4 1.2 - - - -
84A PHE* 3.3 26.0 - - + -
153A PHE* 3.8 30.1 - - + -
169A VAL* 4.4 1.8 - - + -
217A SER* 3.0 14.1 + - - +
218A SER* 1.3 88.4 - - - +
220A LEU* 1.3 61.6 + - - +
221A SER 3.3 0.3 + - - -
223A GLY* 3.3 25.8 - - - +
224A PHE* 3.8 26.9 - - + -
105G ASN* 4.1 12.8 - - + +
106G SER 3.9 22.0 - - - +
107G ILE* 3.8 24.9 - - + -
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Residues in contact with LEU 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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63A GLY 3.1 11.1 - - - -
65A TYR* 3.1 35.5 + - + +
80A TRP* 3.6 33.0 - - + -
81A PRO* 3.3 21.6 - - + +
153A PHE* 3.8 12.1 - - + -
171A PHE* 4.4 3.4 - - + -
174A MET* 3.8 19.7 - - - -
196A PHE* 3.6 28.7 - - + -
216A ALA* 3.8 10.8 - - + -
217A SER* 2.9 23.5 + - - +
219A LEU* 1.3 78.0 - - - +
221A SER* 1.3 58.2 + - - +
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Residues in contact with SER 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ALA* 4.7 0.2 - - - +
63A GLY 2.9 21.5 + - - -
64A GLN* 3.2 6.6 + - - -
65A TYR* 3.9 15.7 - - - +
213A PRO* 4.0 33.3 + - - +
217A SER 4.5 1.0 + - - -
218A SER* 3.3 9.8 + - - -
220A LEU* 1.3 79.5 - - - +
222A SER* 1.3 69.6 + - - +
223A GLY 3.2 0.9 - - - -
156G ILE* 6.1 1.0 - - - +
159G SER* 3.8 4.0 + - - -
168G LYS* 5.9 0.7 + - - -
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Residues in contact with SER 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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60A THR* 4.5 2.9 + - - -
62A ALA* 3.9 2.4 - - - -
63A GLY 3.9 0.2 - - - -
218A SER 3.0 4.7 + - - -
221A SER* 1.3 85.0 + - - +
223A GLY* 1.3 59.3 + - - +
105G ASN* 3.5 10.5 + - - -
156G ILE* 3.2 20.8 - - - +
157G LEU 3.2 23.8 + - - +
158G GLU* 4.0 10.5 + - - -
159G SER* 2.6 33.1 + - - +
168G LYS* 4.4 10.7 + - - -
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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