Contacts of the helix formed by residues 159 - 171 (chain A) in PDB entry 3HB8
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 ASP 159 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A ARG* 3.1 51.0 + - - +
141A HIS* 5.7 1.2 - - - -
157A GLY 4.1 1.4 + - - -
158A VAL* 1.3 75.3 - - - +
160A GLN* 1.3 62.9 + - - +
161A LEU* 3.5 2.9 + - - +
162A GLN* 3.0 28.5 + - + +
163A LYS* 2.9 19.9 + - - +
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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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138A GLN 2.8 25.2 + - - +
139A TRP* 2.9 11.4 + - - +
142A PHE* 3.5 8.2 - - + -
158A VAL* 3.3 18.3 + - + +
159A ASP* 1.3 72.1 - - - +
161A LEU* 1.3 53.3 + - - +
163A LYS* 3.2 8.4 + - + +
164A VAL* 2.7 39.6 + - - +
178A ILE 3.9 6.3 - - - +
179A MET* 3.5 21.3 - - + +
180A CYS 2.7 47.3 + - - +
182B TRP* 4.6 0.2 + - - -
184B PRO* 3.4 24.3 - - + +
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Residues in contact with LEU 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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92A ILE* 3.7 37.7 - - + -
139A TRP* 3.2 15.5 + - + +
140A ARG* 3.8 23.3 - - + +
159A ASP* 3.1 7.7 + - - +
160A GLN* 1.3 79.1 - - - +
162A GLN* 1.3 63.6 + - - +
164A VAL* 3.2 3.8 + - + +
165A ILE* 3.1 30.4 + - + +
179A MET* 3.7 26.1 - - + -
233A LEU* 4.4 12.1 - - + -
237A ILE* 4.3 22.7 - - + -
288A ILE* 4.1 14.8 - - + -
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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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140A ARG* 4.2 5.9 + - - +
159A ASP* 3.0 26.8 + - + +
161A LEU* 1.3 80.9 - - - +
163A LYS* 1.3 52.4 + - - +
165A ILE* 3.1 15.4 + - - +
166A ASP* 2.6 72.7 + - - +
287A LYS* 6.0 1.2 - - - +
288A ILE* 4.2 18.5 + - - +
289A ASP* 4.8 3.3 - - - +
51D THR 3.3 24.7 + - - +
52D GLY* 3.5 16.6 + - - +
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Residues in contact with LYS 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A VAL* 4.3 20.9 - - + -
159A ASP 2.9 17.1 + - - +
160A GLN* 3.5 6.5 - - - +
162A GLN* 1.3 77.5 - - - +
164A VAL* 1.3 50.8 + - + +
166A ASP* 3.1 9.7 + - + +
167A THR* 2.6 51.5 + - - +
176A ARG 5.9 0.8 + - - -
187B LEU* 5.3 13.6 - - - +
188B PRO* 6.5 0.2 - - - -
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Residues in contact with VAL 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A GLN 2.7 23.4 + - - +
161A LEU* 3.5 7.0 - - - +
163A LYS* 1.3 71.1 - - + +
165A ILE* 1.3 67.1 + - - +
167A THR* 3.2 6.3 + - - -
168A ILE* 3.0 30.0 + - + +
177A ILE* 3.9 11.7 - - + +
178A ILE 3.7 37.0 - - - +
179A MET* 4.3 8.5 - - + -
201A PHE* 3.4 35.9 - - + -
237A ILE* 4.5 11.0 - - + -
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Residues in contact with ILE 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 LEU* 3.1 19.2 + - + +
162A GLN* 3.4 16.8 - - - +
164A VAL* 1.3 76.2 - - - +
166A ASP* 1.3 63.7 + - - +
168A ILE* 3.1 19.9 + - - +
169A LYS* 3.3 12.8 + - - +
237A ILE* 4.0 32.1 - - + -
240A ILE* 4.1 8.5 - - + -
241A THR* 3.9 13.2 - - + -
288A ILE* 3.7 36.3 - - + +
51D THR* 3.5 31.6 - - + +
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Residues in contact with ASP 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* 2.6 56.5 + - - +
163A LYS* 3.5 9.2 - - + +
165A ILE* 1.3 71.9 - - - +
167A THR* 1.3 63.7 + - - +
169A LYS* 3.3 3.3 + - - +
170A THR* 3.2 29.4 + - - +
46D ARG* 5.5 0.5 + - - -
53D THR* 3.1 49.0 + - + +
260D ASN* 4.2 10.5 - - - +
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Residues in contact with THR 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 LYS* 2.6 39.7 + - - +
164A VAL* 3.7 5.4 - - - -
165A ILE 3.2 0.2 - - - -
166A ASP* 1.3 72.4 - - - +
168A ILE* 1.3 66.7 + - - +
170A THR* 4.0 5.2 - - - -
171A ASN* 2.8 41.0 + - + +
174A ASP* 3.8 19.7 - - + +
176A ARG 5.9 0.2 - - - -
177A ILE* 3.3 32.2 - - + -
260D ASN* 4.6 4.6 + - - +
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Residues in contact with ILE 168 (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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164A VAL* 3.0 23.6 + - + +
165A ILE* 3.1 11.4 + - - +
167A THR* 1.3 76.7 - - - +
169A LYS* 1.3 61.4 + - - +
171A ASN 5.1 0.2 - - - -
172A PRO* 3.4 22.6 - - - +
177A ILE* 3.7 23.3 - - + -
201A PHE* 4.1 8.3 - - + -
203A VAL* 3.7 22.9 - - + -
208A LEU* 3.8 16.4 - - + -
237A ILE* 4.4 11.0 - - + -
241A THR* 4.0 15.7 - - + +
243A LEU* 3.4 32.6 - - + +
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Residues in contact with LYS 169 (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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165A ILE 3.3 7.1 + - - +
166A ASP 3.3 7.5 + - - +
167A THR 3.1 0.2 - - - -
168A ILE* 1.3 83.0 - - - +
170A THR* 1.3 66.9 + - + +
171A ASN 3.8 0.2 + - - -
172A PRO* 3.9 6.1 - - - +
240A ILE 5.2 0.2 - - - +
241A THR* 4.1 23.8 - - + +
49D ASP* 2.8 27.4 + - - -
50D ARG* 6.1 0.4 - - - +
51D THR* 2.9 34.9 + - + +
53D THR* 3.8 12.3 - - - +
258D TYR* 3.3 21.8 + - + +
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Residues in contact with THR 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 ASP 3.2 13.4 + - - +
167A THR* 3.9 1.2 + - - -
169A LYS* 1.3 78.0 - - + +
171A ASN* 1.3 78.6 + - - +
172A PRO* 3.7 3.4 - - - +
53D THR* 4.4 6.5 - - + -
258D TYR* 3.8 42.4 - - + -
260D ASN* 2.9 32.1 + - + +
261D HIS* 3.0 34.0 + - - -
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Residues in contact with ASN 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 THR* 2.8 27.0 + - + +
170A THR* 1.3 100.4 + - - +
172A PRO* 1.3 59.2 - - - +
173A ASP* 3.2 3.8 - - + -
174A ASP* 3.0 39.2 + - + +
177A ILE* 4.3 0.9 - - - +
260D ASN* 3.6 23.0 + - - +
261D HIS* 4.1 9.7 - - - -
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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