Contacts of the helix formed by residues 141 - 155 (chain D) in PDB entry 2HEO
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 PRO 141 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135D VAL* 5.4 1.6 - - + -
140D VAL* 1.3 103.8 - - + +
142D LYS* 1.3 65.8 + - - +
143D LYS* 4.3 8.7 - - + +
144D THR* 3.2 16.3 + - - +
145D LEU* 3.2 17.7 + - - +
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Residues in contact with LYS 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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131D ILE* 3.7 34.5 - - + +
135D VAL* 4.2 19.0 - - + +
140D VAL 3.7 1.2 + - - -
141D PRO* 1.3 71.5 - - - +
143D LYS* 1.3 58.9 + - - +
145D LEU* 3.3 5.6 + - - +
146D ASN* 2.8 45.0 + - - +
164D LYS* 4.6 6.4 - - - +
202E G 3.0 27.6 + - - -
203E C 4.0 18.8 - - - -
204E G 3.9 5.6 - - - +
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Residues in contact with LYS 143 (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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141D PRO* 3.3 6.3 - - + +
142D LYS* 1.3 76.8 - - - +
144D THR* 1.3 54.5 + - - +
146D ASN* 3.2 2.8 + - - +
147D GLN* 2.8 63.3 + - - +
204E G 3.3 33.7 + - - +
205E C 3.9 15.7 + - - -
206E G 5.5 3.8 + - - -
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Residues in contact with THR 144 (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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114D LEU* 3.6 20.9 - - + -
140D VAL* 3.7 16.2 - - + +
141D PRO* 3.2 24.2 + - - +
143D LYS* 1.3 79.2 - - - +
145D LEU* 1.3 61.4 + - - +
147D GLN* 3.6 17.5 + - - +
148D VAL* 3.2 25.2 + - + +
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Residues in contact with LEU 145 (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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114D LEU* 4.1 12.1 - - + -
118D ILE* 3.5 31.3 - - + +
131D ILE* 4.0 11.9 - - + -
134D LEU* 3.5 38.6 - - + +
135D VAL* 3.6 13.0 - - + +
138D CYS* 4.0 18.4 - - + -
140D VAL* 3.6 23.1 - - + +
141D PRO 3.2 6.9 + - - +
142D LYS 3.6 6.3 - - - +
144D THR* 1.3 77.7 - - - +
146D ASN* 1.3 52.3 + - - +
148D VAL* 3.0 4.7 + - - +
149D LEU* 2.7 43.2 + - + +
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Residues in contact with ASN 146 (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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131D ILE* 3.6 17.2 - - - +
142D LYS* 2.8 33.2 + - - +
143D LYS 3.5 0.4 - - - +
145D LEU* 1.3 70.1 - - - +
147D GLN* 1.3 65.5 + - - +
149D LEU* 4.1 3.3 - - - +
150D TYR* 2.9 51.0 + - + +
166D TRP* 4.0 10.2 + - - -
203E C 3.7 19.4 + - - -
204E G 2.8 44.4 + - - +
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Residues in contact with GLN 147 (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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143D LYS* 2.8 45.4 + - + +
144D THR* 3.6 19.4 + - - +
146D ASN* 1.3 71.1 - - - +
148D VAL* 1.3 63.0 + - + +
150D TYR* 4.5 0.7 - - - +
151D ARG* 3.3 21.8 + - - +
204E G 3.4 24.6 - - - +
205E C 2.7 21.0 + - - +
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Residues in contact with VAL 148 (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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113D ASN* 4.7 8.3 - - + +
114D LEU* 3.9 21.8 - - + -
115D GLU* 4.1 31.9 - - + -
118D ILE* 3.9 17.3 - - + -
144D THR* 3.2 18.1 + - + +
145D LEU 3.0 6.2 + - - +
147D GLN* 1.3 76.9 - - + +
149D LEU* 1.3 61.4 + - - +
151D ARG* 3.3 14.9 + - - +
152D LEU* 2.9 32.7 + - + +
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Residues in contact with LEU 149 (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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118D ILE* 3.7 29.4 - - + -
122D LEU* 4.5 7.0 - - + -
131D ILE* 3.6 29.8 - - + -
134D LEU* 4.3 9.9 - - + -
145D LEU* 2.7 30.0 + - + +
146D ASN* 3.9 4.3 - - - +
148D VAL* 1.3 73.2 - - - +
150D TYR* 1.3 58.6 + - - +
152D LEU* 3.3 4.9 + - + -
153D LYS* 2.8 25.5 + - - +
158D VAL* 3.4 14.0 - - + +
166D TRP* 3.6 52.9 - - + +
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Residues in contact with TYR 150 (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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146D ASN* 2.9 37.8 + - - +
147D GLN 4.6 0.9 - - - +
149D LEU* 1.3 69.3 - - - +
151D ARG* 1.3 63.5 + - - +
153D LYS* 3.4 9.3 + - + +
154D LYS* 3.1 23.9 + - - +
160D SER* 5.4 4.0 + - - -
164D LYS 5.8 0.9 + - - -
166D TRP* 3.5 32.6 - + - -
202E G 4.3 0.9 + - - -
203E C 2.6 34.1 + - - -
204E G 3.5 50.0 + + + +
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Residues in contact with ARG 151 (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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113D ASN* 4.3 9.0 - - - +
115D GLU* 2.6 45.7 + - - +
147D GLN 3.3 20.3 + - - +
148D VAL* 3.5 13.1 - - - +
149D LEU 3.3 0.4 - - - -
150D TYR* 1.3 72.2 - - - +
152D LEU* 1.3 73.6 + - - +
154D LYS* 3.2 7.9 + - - +
155D GLU* 2.5 78.3 + - + +
157D ARG* 3.7 4.8 - - - +
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Residues in contact with LEU 152 (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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115D GLU* 3.6 18.2 - - + +
118D ILE* 4.2 18.2 - - + -
119D LEU* 3.9 15.9 - - + -
148D VAL* 2.9 37.5 + - + +
149D LEU* 3.6 5.6 - - - +
151D ARG* 1.3 80.3 - - - +
153D LYS* 1.3 62.7 + - - +
155D GLU* 3.0 13.1 + - - +
157D ARG* 2.9 64.6 + - + +
158D VAL* 3.6 29.6 - - + -
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Residues in contact with LYS 153 (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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149D LEU 2.8 17.2 + - - +
150D TYR* 3.6 14.8 - - + +
151D ARG 3.2 0.2 - - - -
152D LEU* 1.3 77.0 - - - +
154D LYS* 1.3 57.5 + - - +
156D ASP* 3.2 21.0 + - - +
158D VAL* 3.4 24.1 - - + +
159D SER* 5.1 2.7 - - - -
160D SER 5.6 0.4 - - - +
166D TRP* 4.1 11.2 - - + -
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Residues in contact with LYS 154 (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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150D TYR 3.1 14.0 + - - +
151D ARG* 3.2 6.7 + - - +
153D LYS* 1.3 79.1 - - - +
155D GLU* 1.3 70.4 + - - +
156D ASP* 3.2 7.9 + - - +
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Residues in contact with GLU 155 (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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151D ARG* 2.5 57.5 + - + +
152D LEU* 3.0 9.4 + - - +
154D LYS* 1.3 87.5 - - - +
156D ASP* 1.3 69.4 + - - +
157D ARG* 3.3 33.5 + - - +
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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