Contacts of the helix formed by residues 165 - 171 (chain l) in PDB entry 6QX2
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 PRO 165 (chain l).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164l PHE* 1.4 84.1 - - + +
166l ASN* 1.3 58.1 + - - +
167l LEU* 3.5 2.8 + - - -
168l LEU* 3.8 5.5 + - + -
169l ALA* 3.2 25.5 + - - +
188l LEU* 4.0 11.2 - - + -
191l LEU* 3.7 28.6 - - + +
192l ILE* 4.2 13.7 - - + -
195l VAL* 4.7 9.0 - - + -
352l LEU* 5.4 5.6 - - + -
355l TYR* 3.2 41.7 - - + +
473l LEU* 4.5 1.8 - - + -
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Residues in contact with ASN 166 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39l ARG 5.1 2.0 + - - -
40l ASP* 3.0 28.9 + - - +
41l GLY 4.1 5.1 + - - -
42l LEU* 3.5 22.0 - - - +
99l TYR* 5.6 0.6 - - - -
103l LEU* 4.0 7.1 - - - +
135l LEU* 3.9 21.7 - - + +
164l PHE* 3.0 25.7 + - + +
165l PRO* 1.3 70.7 - - - +
167l LEU* 1.3 66.7 + - - +
169l ALA* 4.0 1.1 - - - -
170l ASN* 2.8 55.2 + - - +
171l GLY 3.8 1.1 + - - +
355l TYR* 4.9 0.6 - - - -
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Residues in contact with LEU 167 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36l PRO* 3.7 31.2 - - + -
37l ASP 4.3 1.6 - - - +
38l VAL* 4.0 40.2 - - + +
39l ARG 5.5 1.0 + - - +
41l GLY* 3.5 28.7 - - - +
165l PRO 3.5 1.0 - - - -
166l ASN* 1.3 77.4 - - - +
168l LEU* 1.3 62.4 + - + +
171l GLY* 2.9 31.8 + - - +
172l ALA* 4.4 4.5 - - + -
183l ILE* 3.9 23.8 - - + +
337l ALA* 4.2 9.2 - - + -
346l ILE* 4.6 7.4 - - + -
351l ALA* 4.8 9.2 - - + +
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Residues in contact with LEU 168 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165l PRO* 3.8 6.1 + - + +
166l ASN 3.3 0.2 - - - -
167l LEU* 1.3 83.2 - - + +
169l ALA* 1.3 62.9 + - - +
183l ILE* 4.1 15.0 - - + -
184l PRO 3.4 2.6 - - - +
185l PRO* 3.4 5.0 - - - +
186l HIS* 2.8 49.1 + - + +
191l LEU* 3.8 21.5 - - + -
234l TYR* 6.1 0.2 - - + -
335l MET* 4.5 13.2 - - - -
348l LEU* 3.9 21.5 - - + -
351l ALA* 4.1 23.6 - - + +
352l LEU* 3.8 30.1 - - + +
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Residues in contact with ALA 169 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100l ARG* 3.6 6.1 - - - +
101l TYR* 4.1 19.5 - - + -
164l PHE* 4.2 13.0 - - + -
165l PRO 3.2 21.8 + - - +
166l ASN* 3.4 8.9 + - - +
168l LEU* 1.3 76.1 - - - +
170l ASN* 1.3 58.9 + - + +
185l PRO* 3.3 6.8 - - - +
186l HIS 3.0 28.2 + - - +
188l LEU* 4.5 4.3 - - + -
191l LEU* 3.4 15.0 - - + +
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Residues in contact with ASN 170 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98l SER 4.8 8.0 - - - +
99l TYR* 3.3 28.1 - - + -
100l ARG* 3.1 10.0 + - - -
101l TYR* 2.8 51.9 + - - +
103l LEU* 3.7 9.9 - - - +
164l PHE* 4.6 2.4 - - - -
166l ASN* 2.8 35.6 + - - +
169l ALA* 1.3 77.1 - - - +
171l GLY* 1.3 64.1 + - - +
185l PRO* 3.5 16.9 - - - +
266l PHE* 5.5 1.4 - - - -
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Residues in contact with GLY 171 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41l GLY 4.7 6.1 - - - +
99l TYR* 5.7 2.6 + - - -
166l ASN* 4.5 1.6 + - - +
167l LEU 2.9 23.3 + - - +
168l LEU 3.8 0.4 + - - -
169l ALA 3.5 1.8 - - - -
170l ASN* 1.3 86.3 - - - +
172l ALA* 1.3 66.2 + - - +
183l ILE* 3.2 17.3 - - - -
184l PRO 3.9 11.2 - - - -
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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