Contacts of the helix formed by residues 176 - 189 (chain A) in PDB entry 4N3Z
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 GLU 176 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A ILE* 1.3 77.0 - - - +
177A GLU* 1.3 61.0 + - - +
178A GLN 3.5 0.2 - - - -
179A SER* 3.8 10.8 + - - -
180A GLU* 3.6 19.2 + - - +
340A ARG* 6.1 1.6 - - - -
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Residues in contact with GLU 177 (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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170A LYS* 4.0 31.9 - - + +
171A ARG* 5.5 0.7 - - - -
173A LEU 5.4 2.0 - - - +
175A ILE* 3.1 5.0 - - - +
176A GLU* 1.3 76.6 - - - +
178A GLN* 1.3 61.8 + - - +
179A SER 3.2 0.4 + - - -
180A GLU* 3.4 6.4 + - - +
181A CYS* 3.0 28.8 + - - +
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Residues in contact with GLN 178 (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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167A MET* 5.9 4.0 - - + -
170A LYS* 6.0 1.3 - - - -
171A ARG* 4.0 27.6 - - + +
175A ILE* 3.4 9.8 + - - +
177A GLU* 1.3 76.0 - - - +
179A SER* 1.3 59.5 + - - +
181A CYS* 3.1 17.0 - - - -
182A ALA* 3.0 29.6 + - - +
341A PHE* 5.3 0.4 - - - +
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Residues in contact with SER 179 (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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175A ILE 3.9 4.1 + - - -
176A GLU* 3.8 14.8 + - - -
177A GLU 3.2 0.4 - - - -
178A GLN* 1.3 79.7 - - - +
180A GLU* 1.3 56.3 + - - +
182A ALA* 3.9 2.4 - - - +
183A GLN* 3.0 30.1 + - - +
340A ARG* 3.4 46.9 - - - +
341A PHE* 5.3 0.7 - - - -
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Residues in contact with GLU 180 (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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176A GLU 3.6 9.7 + - - +
177A GLU* 3.4 9.0 + - - +
179A SER* 1.3 76.0 - - - +
181A CYS* 1.3 59.6 + - - +
183A GLN* 3.8 5.8 - - - +
184A ASP* 2.9 29.8 + - - +
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Residues in contact with CYS 181 (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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163A PHE* 5.4 7.6 - - - +
166A GLY 6.0 1.3 - - - -
167A MET* 5.2 16.8 - - - -
170A LYS* 6.1 5.6 - - + -
177A GLU 3.0 13.4 + - - +
178A GLN* 3.1 25.8 - - - -
180A GLU* 1.3 75.6 - - - +
182A ALA* 1.3 74.6 + - - +
184A ASP* 3.3 6.4 + - - +
185A PHE* 2.9 28.2 + - - +
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Residues in contact with ALA 182 (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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178A GLN 3.0 14.9 + - - +
179A SER 3.9 1.1 - - - +
181A CYS* 1.3 84.6 - - - +
183A GLN* 1.3 59.0 + - - +
185A PHE* 3.2 8.6 + - - +
186A TYR* 2.9 28.6 + - - +
341A PHE* 3.8 32.8 - - + -
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Residues in contact with GLN 183 (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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179A SER 3.0 18.2 + - - +
180A GLU* 3.9 7.4 - - - +
182A ALA* 1.3 76.9 - - - +
184A ASP* 1.3 56.9 + - - +
186A TYR* 3.4 6.8 + - - +
187A HIS* 2.9 29.2 + - - +
340A ARG 5.7 1.1 - - - +
341A PHE* 5.7 0.4 - - - +
344A PRO* 5.7 12.1 - - + -
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Residues in contact with ASP 184 (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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180A GLU 2.9 19.1 + - - +
181A CYS* 3.6 7.9 - - - +
182A ALA 3.2 0.2 - - - -
183A GLN* 1.3 76.6 - - - +
185A PHE* 1.3 59.7 + - - +
187A HIS* 3.2 7.5 + - - +
188A ASN* 3.0 31.1 + - - +
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Residues in contact with PHE 185 (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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163A PHE* 5.0 16.4 - - + -
181A CYS 2.9 13.6 + - - +
182A ALA* 3.2 12.5 + - - +
184A ASP* 1.3 77.6 - - - +
186A TYR* 1.3 60.1 + - - +
188A ASN* 3.6 6.1 + - - +
189A VAL* 3.5 19.9 + - - +
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Residues in contact with TYR 186 (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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182A ALA 2.9 16.5 + - - +
183A GLN* 3.8 7.4 - - - +
185A PHE* 1.3 75.7 - - - +
187A HIS* 1.3 62.7 + - - +
188A ASN 3.6 0.2 + - - -
189A VAL* 3.7 17.5 + - - +
208A MET* 6.4 1.1 - - + -
343A ASN* 3.9 35.4 + - + +
344A PRO* 5.9 0.2 - - + -
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Residues in contact with HIS 187 (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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183A GLN 2.9 17.7 + - - +
184A ASP* 3.2 8.7 + - - +
186A TYR* 1.3 76.0 - - - +
188A ASN* 1.3 64.1 + - - +
189A VAL 3.6 5.9 + - - +
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Residues in contact with ASN 188 (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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184A ASP 3.0 16.6 + - - +
185A PHE* 3.9 7.6 - - - +
186A TYR 3.3 0.2 - - - -
187A HIS* 1.3 75.4 - - - +
189A VAL* 1.3 66.7 + - - +
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Residues in contact with VAL 189 (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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185A PHE 3.5 13.5 + - - +
186A TYR* 3.7 13.4 + - - +
187A HIS 3.4 6.3 - - - +
188A ASN* 1.3 84.6 - - - +
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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