Contacts of the helix formed by residues 170 - 178 (chain M) in PDB entry 5X6E
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 THR 170 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168M ASN* 3.9 16.8 + - - +
169M LEU* 1.3 77.8 - - - +
171M MET* 1.3 63.6 + - - +
172M GLN* 3.6 20.9 - - + +
173M GLU* 3.1 35.7 + - - +
174M LEU* 3.3 9.2 + - - +
7P C 4.0 32.7 + - - +
8P A 3.7 12.3 - - - +
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Residues in contact with MET 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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169M LEU 3.6 0.6 + - - +
170M THR* 1.3 71.1 - - - +
172M GLN* 1.3 63.5 + - - +
173M GLU 3.1 1.3 - - - -
174M LEU* 3.5 6.8 + - + +
175M GLY 3.4 15.6 + - - -
183M SER* 3.2 30.5 - - - +
186M VAL* 3.6 32.0 - - + +
187M SER* 3.3 24.9 - - - +
190M ILE* 4.1 19.3 - - + -
206M PHE* 4.9 14.8 - - + -
8P A 3.1 35.0 + - - +
9P T 3.3 32.1 - - + -
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Residues in contact with GLN 172 (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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170M THR* 3.4 12.5 - - + +
171M MET* 1.3 77.2 - - - +
173M GLU* 1.3 61.0 + - - +
175M GLY* 3.7 2.0 + - - +
176M TYR* 3.0 63.9 + - + +
181M ALA 5.9 3.0 + - - +
182M HIS 6.0 0.4 - - - -
183M SER* 3.8 31.6 + - - +
186M VAL* 5.7 0.7 - - - -
7P C 4.1 16.1 + - - +
8P A 4.2 2.3 + - - +
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Residues in contact with GLU 173 (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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47M LYS* 3.1 37.4 + - - +
59M ASN* 3.8 6.0 + - - -
62M TYR* 2.7 28.1 + - - +
88M ILE* 3.8 11.1 - - - +
169M LEU* 4.4 11.2 - - + -
170M THR* 3.1 32.0 + - - +
171M MET 3.1 0.2 - - - -
172M GLN* 1.3 77.3 - - - +
174M LEU* 1.3 62.7 + - - +
176M TYR* 3.1 17.7 + - - +
177M SER* 3.0 19.6 + - - -
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Residues in contact with LEU 174 (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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62M TYR* 5.6 1.1 - - - +
143M ILE* 4.6 10.5 - - + +
146M GLN* 5.1 10.5 - - + +
147M LEU* 4.7 22.4 - - + -
150M LEU* 4.1 14.1 - - + -
169M LEU* 3.6 40.2 - - + -
170M THR 3.3 6.3 + - - +
171M MET* 3.5 12.1 + - + +
172M GLN 3.4 0.2 - - - -
173M GLU* 1.3 76.4 - - + +
175M GLY* 1.3 66.7 + - - +
177M SER* 3.0 8.3 + - - -
178M SER* 2.9 23.9 + - - -
186M VAL* 4.7 6.1 - - + -
190M ILE* 4.6 18.8 - - + -
206M PHE* 4.5 19.5 - - + -
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Residues in contact with GLY 175 (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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171M MET 3.4 8.1 + - - -
172M GLN 3.7 3.8 + - - -
173M GLU 3.3 0.4 - - - -
174M LEU* 1.3 77.5 - - - +
176M TYR* 1.3 61.2 + - - +
178M SER* 2.9 28.2 + - - +
179M GLY 3.8 0.2 - - - -
180M ILE* 2.7 27.5 + - - +
186M VAL* 3.7 21.6 - - - +
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Residues in contact with TYR 176 (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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47M LYS* 4.9 2.5 - - - -
57M ILE* 3.3 40.5 - - + +
58M MET* 3.7 6.6 - - - +
59M ASN* 3.1 35.0 + - - +
172M GLN* 3.0 57.6 + - + -
173M GLU* 3.1 25.7 + - - +
175M GLY* 1.3 76.6 - - - +
177M SER* 1.3 58.3 + - - +
178M SER 2.8 12.8 - - - +
180M ILE 4.4 5.4 - - - -
181M ALA* 5.3 11.4 - - - -
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Residues in contact with SER 177 (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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58M MET* 3.9 4.9 - - - +
59M ASN* 3.4 25.3 + - - +
60M LEU 4.8 0.9 + - - +
61M GLN* 5.5 0.3 - - - -
62M TYR* 3.9 19.4 - - - -
130M LYS* 4.7 1.7 + - - -
134M PHE* 4.3 2.3 - - - -
146M GLN* 2.2 46.0 + - - +
173M GLU 3.0 9.6 + - - -
174M LEU* 3.0 13.7 + - - -
176M TYR* 1.3 70.9 - - - +
178M SER* 1.3 65.9 + - - +
131N PHE* 4.3 10.0 - - - -
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Residues in contact with SER 178 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58M MET* 3.3 12.5 - - - +
134M PHE* 4.1 12.1 - - - -
142M SER* 3.6 26.0 - - - -
143M ILE* 3.4 23.0 - - - +
146M GLN* 5.3 2.6 - - - +
174M LEU 2.9 16.5 + - - -
175M GLY* 2.9 17.4 + - - +
176M TYR 2.8 17.7 - - - +
177M SER* 1.3 76.0 - - - +
179M GLY* 1.3 61.0 + - - +
180M ILE* 3.8 6.6 - - - +
131N PHE* 5.7 0.2 - - - -
135N SER* 5.1 0.7 - - - -
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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