Contacts of the helix formed by residues 157 - 174 (chain A) in PDB entry 2HBH
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 157 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A MET 5.3 0.2 - - - -
156A LEU* 1.3 75.1 - - - +
158A ASP* 1.3 66.0 + - - +
159A GLU* 3.7 7.0 + - - +
160A GLN* 2.7 44.0 + - - +
161A MET* 2.9 24.7 + - - +
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Residues in contact with ASP 158 (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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157A SER* 1.3 73.1 - - - +
159A GLU* 1.3 55.4 + - - +
161A MET* 3.3 11.7 + - - +
162A GLN* 2.8 54.5 + - - +
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Residues in contact with GLU 159 (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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157A SER* 3.3 6.1 + - - +
158A ASP* 1.3 78.0 - - - +
160A GLN* 1.3 65.2 + - + +
162A GLN* 3.2 12.9 + - - +
163A ILE* 3.1 32.8 + - + +
386A ARG* 3.6 32.2 + - - +
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Residues in contact with GLN 160 (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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155A MET 4.6 2.6 + - - -
156A LEU* 3.6 11.3 - - + +
157A SER* 2.7 49.1 + - - +
159A GLU* 1.3 77.8 - - + +
161A MET* 1.3 65.5 + - - +
163A ILE* 2.9 23.0 + - - +
164A ILE* 3.2 9.9 + - - +
389A ASP* 4.6 3.1 - - + +
390A VAL* 3.8 34.5 - - + +
393A ALA* 3.6 27.1 - - - +
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Residues in contact with MET 161 (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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156A LEU* 4.6 15.9 - - + +
157A SER 2.9 20.1 + - - +
158A ASP* 3.8 10.5 - - - +
160A GLN* 1.3 74.2 - - - +
162A GLN* 1.3 89.0 + - + +
164A ILE* 3.0 24.1 + - + +
165A ASN* 3.0 44.9 + - - +
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Residues in contact with GLN 162 (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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158A ASP* 2.8 46.0 + - + +
159A GLU* 3.5 11.4 + - - +
161A MET* 1.3 89.4 - - + +
163A ILE* 1.3 63.0 + - + +
165A ASN* 3.4 7.2 + - - +
166A SER* 3.1 26.5 + - - -
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Residues in contact with ILE 163 (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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159A GLU* 3.1 27.0 + - + +
160A GLN* 2.9 11.5 + - - +
162A GLN* 1.3 77.3 - - + +
164A ILE* 1.3 55.4 + - - +
166A SER* 3.6 5.5 + - - -
167A LEU* 3.1 38.1 + - + +
277A PRO* 3.9 25.1 - - + +
360A LEU* 4.7 3.4 - - + -
386A ARG* 4.0 27.6 - - + -
387A LEU* 3.8 26.2 - - + -
390A VAL* 4.1 22.4 - - + -
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Residues in contact with ILE 164 (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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156A LEU* 3.7 27.6 - - + -
160A GLN 3.5 10.1 - - - +
161A MET* 3.0 11.4 + - + +
163A ILE* 1.3 75.9 - - + +
165A ASN* 1.3 69.3 + - - +
166A SER 3.1 1.6 - - - -
167A LEU* 3.4 4.8 + - - +
168A VAL* 3.0 27.1 + - + +
356A GLU* 3.4 34.5 - - + +
359A VAL* 5.9 0.9 - - + -
360A LEU* 4.4 11.0 - - + -
390A VAL* 3.6 27.6 - - + -
394A TYR* 3.9 17.3 - - + -
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Residues in contact with ASN 165 (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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161A MET* 3.0 47.1 + - - +
162A GLN* 3.4 8.2 + - - +
164A ILE* 1.3 78.2 - - - +
166A SER* 1.3 58.2 + - - +
168A VAL* 4.1 3.6 - - - +
169A GLU* 3.1 33.9 + - - +
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Residues in contact with SER 166 (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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162A GLN 3.1 17.0 + - - -
163A ILE* 3.7 7.6 - - - -
164A ILE 3.1 0.6 - - - -
165A ASN* 1.3 76.5 - - - +
167A LEU* 1.3 55.9 + - - +
169A GLU* 3.3 6.3 + - - +
170A ALA* 2.8 36.0 + - - +
275A MET* 4.5 13.5 - - - +
277A PRO* 4.8 8.5 - - - +
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Residues in contact with LEU 167 (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 ILE* 3.1 25.9 + - + +
164A ILE* 3.4 2.9 + - - +
166A SER* 1.3 72.1 - - - +
168A VAL* 1.3 61.8 + - - +
170A ALA* 3.2 5.1 + - + +
171A HIS 2.8 26.2 + - - -
272A PHE* 3.6 7.0 - - + -
275A MET 4.4 2.2 - - - +
276A ILE* 3.9 16.6 - - + -
277A PRO* 3.7 24.2 - - + -
359A VAL* 3.3 27.3 - - + +
360A LEU* 3.4 36.8 - - + -
363A ALA* 3.9 25.4 - - + -
387A LEU* 4.9 2.2 - - + -
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Residues in contact with VAL 168 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164A ILE* 3.0 20.0 + - + +
165A ASN* 4.3 4.0 - - - +
167A LEU* 1.3 75.2 - - - +
169A GLU* 1.3 62.3 + - - +
171A HIS* 3.9 0.8 - - - +
172A HIS* 3.2 50.7 + - + +
355A GLU* 3.9 13.0 - - - +
356A GLU* 3.9 31.9 - - + +
359A VAL* 3.9 21.3 - - + -
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Residues in contact with GLU 169 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A ASN* 3.1 24.0 + - - +
166A SER* 3.7 5.0 - - - +
168A VAL* 1.3 74.5 - - - +
170A ALA* 1.3 67.1 + - - +
172A HIS* 3.3 9.6 + - + +
173A LYS* 3.0 52.6 + - - +
275A MET* 6.2 0.9 - - - -
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Residues in contact with ALA 170 (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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166A SER 2.8 19.0 + - - +
167A LEU* 3.5 7.4 - - + +
169A GLU* 1.3 78.3 - - - +
171A HIS* 1.3 58.6 + - - +
173A LYS* 3.5 1.5 + - - +
174A THR* 2.8 31.7 + - - +
272A PHE* 3.7 18.8 - - + +
275A MET* 3.6 42.8 - - + +
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Residues in contact with HIS 171 (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 LEU 2.8 7.1 + - - +
168A VAL* 3.9 4.5 - - - +
170A ALA* 1.3 74.2 - - - +
172A HIS* 1.3 63.4 + + - +
174A THR* 2.9 10.5 + - - -
175A TYR* 2.9 55.1 + + + +
272A PHE* 3.8 6.3 - - + -
302A ARG* 4.8 6.7 + - + -
305A GLN* 2.8 40.5 + - - -
355A GLU* 4.2 22.2 - - + -
358A HIS* 4.2 8.0 - + - -
359A VAL* 3.3 30.1 - - + -
362A MET* 3.7 20.9 - - + +
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Residues in contact with HIS 172 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A VAL* 3.2 33.2 + - + +
169A GLU* 3.7 8.0 - - + +
171A HIS* 1.3 83.2 - + - +
173A LYS* 1.3 61.2 + - - +
174A THR 3.3 1.0 + - - -
175A TYR 3.6 18.4 + - - +
355A GLU* 2.7 39.4 + - - -
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Residues in contact with LYS 173 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A GLU* 3.0 43.3 + - - +
170A ALA* 3.7 6.5 - - - +
171A HIS 3.2 0.2 - - - -
172A HIS* 1.3 76.1 - - - +
174A THR* 1.3 62.9 + - + +
175A TYR 3.8 0.2 - - - -
268A LYS* 5.3 3.5 + - - -
275A MET* 3.9 29.5 - - + -
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Residues in contact with THR 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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170A ALA 2.8 20.6 + - - +
171A HIS* 2.9 10.8 + - - -
173A LYS* 1.3 86.9 - - + +
175A TYR* 1.3 53.2 + - - +
268A LYS* 3.5 46.8 + - + +
271A GLY* 4.1 8.7 - - - -
272A PHE* 3.8 23.5 - - - +
275A MET* 4.3 9.6 - - + -
302A ARG* 2.8 30.0 + - - -
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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