Contacts of the helix formed by residues 134 - 142 (chain D) 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 VAL 134 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90D TRP* 5.0 5.6 - - + -
91D PHE* 5.8 0.2 - - + -
96D THR* 4.3 10.5 - - - +
109D TRP* 4.3 15.7 - - + -
131D LEU* 3.9 40.8 - - + +
132D GLY 2.6 21.6 + - - +
133D PRO* 1.3 75.5 - - - +
135D TYR* 1.3 78.1 + - + +
136D GLY 2.8 4.0 + - - +
137D PHE* 2.6 21.3 + - - +
138D GLN* 3.4 3.7 + - - -
190D MET* 4.0 23.6 - - + -
191D ALA* 4.6 3.4 - - + +
192D LEU 4.6 7.9 - - - +
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Residues in contact with TYR 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D PHE* 3.4 31.4 - + + -
109D TRP* 4.0 33.7 - + - -
134D VAL* 1.3 72.7 - - + +
136D GLY* 1.3 54.7 + - - +
137D PHE 3.1 0.5 + - - -
138D GLN* 3.1 7.1 + - - +
139D TRP* 2.7 57.7 + + - +
181D ALA* 4.7 8.7 - - + +
190D MET* 6.6 0.2 - - - -
192D LEU 5.3 3.1 - - - -
194D PRO* 3.7 22.9 - - + +
195D CYS* 2.7 32.1 + - - +
196D HIS* 3.2 45.7 + + + -
230D TYR* 4.5 3.8 - - - -
565D UMP 5.3 0.5 + - - -
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Residues in contact with GLY 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D PHE* 3.8 29.8 - - - -
94D GLY* 3.7 9.7 - - - -
95D SER 4.1 15.0 + - - -
134D VAL* 2.8 6.7 + - - +
135D TYR* 1.3 77.7 - - - +
137D PHE* 1.3 58.5 + - - -
139D TRP* 3.4 5.5 - - - +
140D ARG* 3.3 26.3 + - - +
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Residues in contact with PHE 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D GLY 4.3 7.0 + - - -
95D SER 5.0 1.0 + - - -
96D THR* 4.9 8.1 - - + -
132D GLY 4.5 3.1 - - - +
133D PRO* 3.5 30.1 - - + -
134D VAL 2.6 16.7 + - - +
136D GLY* 1.3 67.4 - - - +
138D GLN* 1.3 67.4 + - - +
139D TRP 3.0 1.7 + - - -
140D ARG 3.2 0.5 + - - -
141D HIS* 2.8 56.4 + + + +
143D GLY 5.7 0.7 - - - -
144D ALA* 3.5 26.0 - - + -
145D GLU 4.2 4.0 - - - -
146D TYR* 3.3 37.2 - + + -
153D TYR* 3.4 39.9 - + - -
186D ASP* 4.5 5.6 - - - -
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Residues in contact with GLN 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D PRO* 2.7 37.0 + - - +
134D VAL 4.2 6.1 - - - +
135D TYR 3.1 6.6 + - - +
137D PHE* 1.3 85.1 - - - +
139D TRP* 1.3 61.1 + - - +
142D PHE* 3.0 49.4 + - + +
160D GLN* 3.0 23.1 + - - -
181D ALA* 3.5 31.0 - - + +
183D ASN* 3.3 13.7 + - - +
186D ASP* 3.0 28.6 + - - +
190D MET* 3.9 2.0 - - + +
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Residues in contact with TRP 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D LEU* 4.2 9.6 - - + -
91D PHE* 3.6 46.0 - + + +
92D ILE* 4.3 11.4 - - + -
135D TYR* 2.7 41.5 + + + +
136D GLY* 3.4 7.9 - - - +
137D PHE 3.0 0.2 - - - -
138D GLN* 1.3 80.5 - - - +
140D ARG* 1.3 65.0 + - - +
160D GLN 3.2 22.5 + - - -
161D LEU* 3.3 33.9 + - + -
179D MET* 3.2 30.6 + - + +
180D CYS 5.6 1.8 - - - -
181D ALA* 4.6 14.1 - - + +
199D CYS* 5.8 0.7 - - - -
230D TYR* 3.7 28.0 + + - -
233D LEU* 3.9 26.7 - - + -
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Residues in contact with ARG 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D PHE 4.6 1.6 - - - -
92D ILE* 2.5 36.2 + - - +
93D LYS 4.9 1.3 - - - +
94D GLY* 3.8 17.7 - - - -
136D GLY 3.3 12.3 + - - +
137D PHE 3.2 2.2 + - - -
139D TRP* 1.3 87.0 - - + +
141D HIS* 1.3 90.4 + - + +
156D GLN 4.3 0.9 - - - +
157D GLY 4.7 0.2 - - - -
158D VAL 3.4 5.1 - - - -
159D ASP* 2.9 59.6 + - - +
161D LEU* 3.2 31.4 - - - +
162D GLN* 4.6 9.3 - - - +
288D ILE* 4.7 4.4 - - - +
289D ASP* 3.6 24.8 + - - -
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Residues in contact with HIS 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D GLY* 5.4 7.8 + - - -
137D PHE* 2.8 47.2 + + + -
140D ARG* 1.3 103.9 + - + +
142D PHE* 1.3 66.3 + - - +
143D GLY 3.5 0.3 + - - -
144D ALA* 3.1 16.3 + - + +
153D TYR* 2.8 52.7 + + + +
154D SER* 4.1 7.4 + - - -
155D GLY 4.7 2.2 + - - -
156D GLN 3.2 16.1 + - - +
157D GLY* 3.8 2.9 - - - -
158D VAL 4.0 0.9 - - - -
159D ASP* 5.7 0.7 - - - -
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Residues in contact with PHE 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D PHE* 5.8 0.2 - - - -
138D GLN* 3.0 47.2 + - + +
141D HIS* 1.3 74.0 - - - +
143D GLY* 1.3 74.9 + - - +
144D ALA 2.9 6.2 + - - -
157D GLY* 3.1 1.6 - - - -
158D VAL* 3.0 38.0 + - + +
160D GLN* 3.2 24.9 - - + +
180D CYS* 3.5 14.6 - - - -
182D TRP 4.1 12.8 - - - -
183D ASN* 3.0 32.3 - - + -
142E PHE* 4.5 6.7 - + - -
182E TRP 5.0 0.9 - - - -
183E ASN* 3.7 13.9 - - - -
184E PRO* 3.4 34.5 - - + -
185E ARG* 4.6 5.4 - - + +
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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