Contacts of the helix formed by residues 148 - 157 (chain B) in PDB entry 7CE1
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 148 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B SER* 5.1 1.4 + - - -
144B ILE* 4.5 0.4 - - + -
145B GLU* 3.4 38.2 + - - +
146B PRO 3.7 2.2 - - - -
147B ASN* 1.3 72.7 - - - +
149B PRO* 1.3 75.0 - - - +
150B ARG* 2.7 71.2 + - - +
151B VAL* 3.4 24.7 + - + -
152B ARG* 3.9 5.0 + - - +
169B MET* 3.0 20.4 - - - +
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Residues in contact with PRO 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B SER* 5.1 8.3 - - - +
124B MET* 3.9 24.6 - - + +
145B GLU* 5.3 6.7 - - - +
147B ASN 3.8 6.7 - - - +
148B ASP* 1.3 93.4 - - - +
150B ARG* 1.3 65.5 + - + +
152B ARG* 3.7 7.7 + - + +
153B PHE* 3.2 24.1 + - - +
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Residues in contact with ARG 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B VAL* 5.6 1.8 - - - +
117B HIS* 5.2 10.1 - - - -
123B SER* 3.7 24.1 + - - +
124B MET* 3.7 30.1 - - + -
127B ILE* 3.6 31.1 - - + +
141B ILE* 3.7 33.1 - - + +
142B SER 3.1 20.0 + - - +
143B LYS* 2.9 26.1 + - - +
144B ILE* 3.8 5.7 - - - +
148B ASP* 2.7 38.1 + - - +
149B PRO* 1.3 78.9 - - + +
151B VAL* 1.3 63.7 + - - +
153B PHE* 3.7 2.0 - - - +
154B MET* 3.2 29.4 + - + +
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Residues in contact with VAL 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B ILE* 4.5 5.2 - - + -
144B ILE* 4.4 11.4 - - + -
148B ASP* 3.4 24.2 + - + +
149B PRO 3.3 1.0 - - - -
150B ARG* 1.3 78.0 - - - +
152B ARG* 1.3 56.4 + - - +
155B THR* 2.6 33.4 + - - +
161B PHE* 3.2 18.1 - - + -
163B THR* 4.4 19.3 - - + -
167B SER* 4.2 2.9 - - - +
169B MET* 3.5 23.8 - - + -
171B ILE* 4.9 1.3 - - + -
173B HIS* 3.4 32.5 - - + +
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Residues in contact with ARG 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ASN* 5.6 6.7 - - - +
148B ASP 3.9 6.0 + - - +
149B PRO* 3.7 9.6 + - + +
150B ARG 3.5 0.2 - - - -
151B VAL* 1.3 77.5 - - - +
153B PHE* 1.3 59.8 + - - +
155B THR* 3.0 3.2 + - - -
156B GLU* 2.7 56.1 + - - +
169B MET* 4.0 30.4 + - + +
171B ILE* 3.4 28.1 - - + +
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Residues in contact with PHE 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B MET* 4.3 11.0 - - + -
127B ILE* 3.8 21.3 - - + -
128B ARG* 3.3 45.5 - - + -
131B LEU* 4.5 12.3 - - + -
149B PRO 3.2 19.4 + - - +
150B ARG* 3.7 6.3 - - - +
151B VAL 3.3 0.2 - - - -
152B ARG* 1.3 79.3 - - - +
154B MET* 1.3 56.3 + - - +
156B GLU* 3.4 16.8 - - - +
157B ARG* 3.0 81.5 + - + +
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Residues in contact with MET 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B ILE* 3.4 46.2 - - + -
131B LEU* 4.4 12.8 - - + -
139B VAL* 3.5 32.3 - - + -
141B ILE* 4.3 8.1 - - + -
150B ARG* 3.2 17.1 + - + +
153B PHE* 1.3 75.1 - - - +
155B THR* 1.3 62.5 + - - +
157B ARG* 4.4 1.6 - - - +
158B LYS 3.2 2.1 + - - -
159B MET* 2.9 44.3 + - + +
161B PHE* 3.4 46.9 - - + -
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Residues in contact with THR 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B VAL 2.6 22.0 + - - -
152B ARG* 3.0 11.8 + - - -
154B MET* 1.3 78.9 - - - +
156B GLU* 1.3 60.5 + - - +
158B LYS* 3.4 11.7 + - - +
159B MET 5.2 0.2 - - - -
161B PHE* 3.3 17.9 - - + -
171B ILE* 3.8 29.1 - - + +
172B GLU 5.5 2.5 - - - +
173B HIS* 5.1 0.7 - - - +
326B ARG* 5.5 9.6 - - - +
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Residues in contact with GLU 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B ARG* 2.7 52.3 + - - +
153B PHE* 3.4 23.9 - - + +
155B THR* 1.3 70.7 - - - +
157B ARG* 1.3 63.2 + - + +
158B LYS* 3.2 7.1 + - - +
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Residues in contact with ARG 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B LEU* 4.1 35.9 + - + +
132B GLU* 5.5 6.3 - - - +
153B PHE* 3.0 62.0 + - + +
154B MET* 4.3 2.9 - - - +
155B THR 3.3 0.2 - - - -
156B GLU* 1.3 80.3 - - + +
158B LYS* 1.3 69.5 + - - +
159B MET* 3.1 4.6 + - - +
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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