Contacts of the helix formed by residues 171 - 181 (chain A) in PDB entry 5H8N
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 GLY 171 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A HIS* 5.4 4.3 - - - -
88A GLY 5.3 0.2 - - - -
120A ARG* 4.4 5.4 - - - -
168A VAL 4.5 1.8 + - - -
169A PRO 3.3 6.3 + - - -
170A ASN* 1.3 80.5 - - - +
172A SER* 1.3 64.2 + - - -
173A THR 3.3 2.9 - - - -
174A GLU* 3.6 2.5 + - - +
175A ARG* 3.4 21.3 + - - +
301A GLU* 3.3 27.4 - - - -
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Residues in contact with SER 172 (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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115A THR* 3.3 25.9 + - - +
117A ASN* 3.6 28.5 + - - +
120A ARG* 4.0 4.4 - - - +
135A ILE* 5.7 0.7 - - - -
171A GLY* 1.3 69.8 - - - -
173A THR* 1.3 64.0 + - - +
175A ARG* 3.6 6.0 - - - +
176A ASN* 3.1 25.1 + - - +
301A GLU* 2.9 30.7 + - - -
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Residues in contact with THR 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A GLY 4.8 0.3 + - - -
135A ILE* 4.0 24.8 - - + +
167A THR* 3.9 15.0 - - - +
172A SER* 1.3 69.2 + - - +
174A GLU* 1.3 64.5 + - - +
176A ASN* 3.4 3.6 + - - +
177A ILE* 3.1 29.9 + - + +
212A ILE* 3.8 33.2 - - + +
213A TYR* 3.9 5.2 - - - -
214A ASP* 3.7 10.6 + - - -
301A GLU* 2.8 38.4 + - - -
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Residues in contact with GLU 174 (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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89A LYS* 5.0 4.3 + - - -
167A THR* 4.1 21.2 + - + -
168A VAL 4.5 1.3 + - - +
169A PRO* 3.5 25.2 - - + +
170A ASN* 2.8 41.6 + - - +
171A GLY 3.6 4.1 + - - +
172A SER 3.5 0.2 - - - -
173A THR* 1.3 77.6 - - - +
175A ARG* 1.3 53.2 + - - +
177A ILE* 3.2 7.1 + - + +
178A ARG* 2.8 35.0 + - + +
185A HIS* 3.2 30.7 + - + +
189A THR* 4.3 9.8 - - + +
192A ASN* 4.6 3.1 + - - +
301A GLU* 4.3 0.6 + - - -
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Residues in contact with ARG 175 (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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90A LYS* 5.8 3.8 - - - +
117A ASN* 5.0 6.7 - - - +
119A GLU* 2.8 46.4 + - + +
171A GLY 3.4 12.9 + - - +
172A SER* 3.6 12.8 - - - +
174A GLU* 1.3 77.0 + - - +
176A ASN* 1.3 56.0 + - - +
178A ARG* 3.1 46.8 + - - +
179A ASN* 3.1 61.4 + - - +
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Residues in contact with ASN 176 (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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135A ILE* 3.4 25.7 - - + +
148A LEU* 5.3 0.2 - - - +
172A SER 3.1 17.8 + - - +
173A THR 3.7 4.9 - - - +
175A ARG* 1.3 72.5 - - - +
177A ILE* 1.3 62.7 + - - +
179A ASN* 3.4 6.8 + - - +
180A ASN* 2.9 45.0 + - - +
181A TYR* 5.0 2.4 - - - -
239A PHE* 3.6 8.0 - - - -
240A ALA* 4.2 7.3 - - - +
274B GLU* 3.1 44.8 + - - +
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Residues in contact with ILE 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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135A ILE* 5.0 4.0 - - + -
148A LEU* 5.2 4.9 - - + -
167A THR* 5.0 2.0 - - + -
173A THR* 3.1 23.0 + - + +
174A GLU* 3.6 10.5 - - + +
176A ASN* 1.3 80.7 - - - +
178A ARG* 1.4 55.6 + - - +
181A TYR* 2.8 42.3 + - + +
184A MET* 3.7 30.5 - - - -
185A HIS* 3.9 19.5 - - + +
188A MET* 3.9 23.6 - - + -
212A ILE* 3.5 32.1 - - + -
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Residues in contact with ARG 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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174A GLU* 2.8 20.2 + - - +
175A ARG* 3.1 40.7 - - - +
176A ASN 3.3 0.2 - - - -
177A ILE* 1.4 74.3 - - - +
179A ASN* 1.3 64.1 + - - +
182A PRO* 4.1 19.6 - - + +
185A HIS* 3.7 38.1 - - + +
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Residues in contact with ASN 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 ARG* 3.1 56.2 + - - +
176A ASN* 3.8 6.9 - - - +
178A ARG* 1.3 81.7 + - - +
180A ASN* 1.3 66.3 + - - +
182A PRO* 4.5 5.7 - - - +
274B GLU* 5.5 4.8 + - - -
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Residues in contact with ASN 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 ASN* 2.9 41.0 + - - +
179A ASN* 1.3 81.0 - - - +
181A TYR* 1.4 85.4 + - + +
182A PRO* 3.6 7.2 - - - +
239A PHE* 4.2 6.5 - - - -
274B GLU 2.7 24.9 + - - -
275B ASN* 3.7 24.1 - - - +
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Residues in contact with TYR 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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148A LEU* 4.1 30.2 - - + +
149A SER* 4.9 6.9 + - - -
154A GLN* 3.2 37.9 - - - +
176A ASN* 5.0 2.7 - - - -
177A ILE* 2.8 25.1 + - + +
180A ASN* 1.4 96.8 - - + +
182A PRO* 1.4 67.8 - - - +
183A TYR 3.4 2.0 - - - -
184A MET* 3.3 36.7 + - + +
185A HIS* 2.9 22.2 + - - +
239A PHE* 4.1 21.2 - + - -
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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