Contacts of the helix formed by residues 168 - 172 (chain M) in PDB entry 2X5V
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 168 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217C GLY 4.9 0.4 - - - -
220C ARG* 4.6 8.7 - - - -
222C PRO* 5.7 0.2 - - - -
99M GLN* 2.6 34.9 + - - -
100M TYR 5.4 0.2 + - - -
101M GLY 3.4 7.8 + - - -
102M MET* 3.6 1.6 - - - -
163M PRO* 2.8 16.3 + - - +
166M VAL* 3.7 3.3 - - - +
167M GLY* 1.3 77.2 - - - +
169M TRP* 1.3 64.5 + - - +
170M SER* 3.0 18.8 + - - -
171M GLU* 3.1 28.3 + - - +
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Residues in contact with TRP 169 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95M PRO* 3.8 8.8 - - - +
96M PRO* 3.8 22.2 - - + -
101M GLY 3.6 9.0 + - - +
102M MET* 3.1 59.7 + - + +
103M GLY 4.6 0.4 - - - -
104M ILE* 5.6 0.6 - - - +
105M PRO* 4.4 15.9 - - + -
113M TRP* 3.5 29.4 - + + -
114M LEU* 3.7 37.9 - - + +
159M GLY 4.2 2.0 - - - -
160M CYS* 3.6 40.2 - - + -
163M PRO* 4.0 9.9 - - + -
164M THR* 4.8 1.3 - - - -
168M SER* 1.3 69.9 - - - +
170M SER* 1.3 61.9 + - - +
171M GLU 2.9 2.8 + - - -
172M GLY* 2.9 15.5 + - - -
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Residues in contact with SER 170 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C PRO* 3.4 18.2 - - - +
223C LEU* 2.9 35.7 + - - +
224C SER 4.9 1.9 + - - -
227C TYR* 5.0 2.6 - - - -
95M PRO* 3.9 9.3 - - - +
96M PRO* 3.2 33.5 - - - +
97M LYS 4.8 0.9 - - - -
98M ALA 5.1 2.7 - - - -
99M GLN* 4.7 0.7 - - - -
168M SER* 3.0 20.0 + - - -
169M TRP* 1.3 76.9 - - - +
171M GLU* 1.3 61.8 + - - +
172M GLY 3.3 6.6 + - - +
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Residues in contact with GLU 171 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220C ARG* 2.7 26.0 + - - -
221C ARG 4.8 2.8 - - - +
222C PRO* 5.0 0.7 - - - +
223C LEU* 3.8 30.4 + - - +
158M ILE 4.9 0.9 - - - +
162M HIS* 2.9 26.4 + - + -
163M PRO* 4.2 5.4 - - + -
166M VAL* 3.7 12.3 - - + -
168M SER* 3.2 22.4 - - - +
169M TRP 2.9 0.6 + - - -
170M SER* 1.3 76.8 + - - +
172M GLY* 1.3 59.5 + - - +
183M TRP* 3.0 26.1 + - - -
187M PHE* 4.0 7.8 - - - -
190M ARG* 5.1 1.7 + - - -
191M TYR* 2.6 30.5 + - - -
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Residues in contact with GLY 172 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C TYR* 4.3 0.7 + - - -
95M PRO* 3.5 15.1 - - - +
113M TRP* 3.7 18.2 - - - -
158M ILE 4.2 6.5 - - - -
159M GLY 4.3 0.7 - - - -
163M PRO* 3.9 11.9 - - - +
169M TRP 2.9 15.6 + - - -
170M SER 3.2 1.4 - - - +
171M GLU* 1.3 83.3 - - - +
173M VAL* 1.3 65.2 + - - -
174M PRO* 3.6 4.3 - - - +
183M TRP* 3.7 5.7 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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