Contacts of the helix formed by residues 167 - 174 (chain D) in PDB entry 7CAL
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 LEU 167 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148D PHE* 4.4 41.9 - - + -
163D GLY* 3.6 22.9 - - - +
164D PHE* 3.8 14.5 + - + +
165D ARG 3.2 0.8 - - - -
166D ILE* 1.3 81.7 - - + +
168D SER* 1.3 57.5 + - - +
169D MET 3.2 0.9 - - - -
170D LEU* 3.4 46.1 + - + +
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Residues in contact with SER 168 (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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77D CYS* 3.3 18.0 + - - -
80D GLN* 4.4 5.7 + - - -
148D PHE* 5.3 2.0 - - - +
149D GLN* 4.8 18.9 - - - +
164D PHE 4.1 2.2 + - - -
165D ARG* 3.2 22.1 + - - -
166D ILE 3.1 1.0 - - - -
167D LEU* 1.3 75.3 - - - +
169D MET* 1.3 57.4 + - - +
170D LEU 3.2 5.5 + - - -
171D ARG* 3.2 34.1 + - - +
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Residues in contact with MET 169 (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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77D CYS* 3.3 35.2 - - - +
78D PRO* 3.7 5.6 - - + -
81D PHE* 3.6 31.0 - - + -
165D ARG 3.8 2.0 + - - +
166D ILE* 2.9 26.9 + - + +
168D SER* 1.3 74.6 - - - +
170D LEU* 1.3 59.2 + - + +
171D ARG 3.1 5.4 - - - -
172D LEU* 3.1 40.5 + - + +
173D TRP* 4.4 2.3 + - - -
215D PHE* 3.6 30.5 - - + -
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Residues in contact with LEU 170 (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 CYS* 3.5 33.0 - - + +
144D SER* 3.1 24.0 + - - -
148D PHE* 5.0 7.4 - - + -
166D ILE 5.0 2.2 - - - +
167D LEU* 3.4 42.2 - - + +
168D SER 3.2 0.8 - - - -
169D MET* 1.3 77.5 - - + +
171D ARG* 1.3 55.9 + - - +
172D LEU 3.1 5.4 - - - -
173D TRP* 3.1 46.4 + - + +
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Residues in contact with ARG 171 (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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72D TYR* 5.7 0.6 - - - -
73D SER* 3.5 32.0 + - - +
74D ALA* 5.2 0.9 - - - +
76D ILE* 3.6 32.5 - - - +
77D CYS* 3.6 30.7 + - - +
80D GLN* 3.4 20.2 - - - +
95D ASP* 4.4 17.3 + - - +
98D VAL* 6.1 2.0 - - - +
99D ASN* 5.4 10.5 - - - +
144D SER* 4.3 5.2 - - - +
168D SER* 3.2 31.9 + - - +
169D MET 3.1 1.4 - - - -
170D LEU* 1.3 75.9 - - - +
172D LEU* 1.3 56.8 + - - +
173D TRP 3.3 1.3 - - - -
174D ARG* 3.3 48.1 - - - +
175D LEU* 5.8 0.2 - - - +
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Residues in contact with LEU 172 (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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74D ALA* 3.8 28.7 - - + +
77D CYS* 4.0 18.6 - - + -
78D PRO* 4.9 3.4 - - + -
169D MET* 3.1 30.7 + - + +
170D LEU 3.1 1.2 - - - -
171D ARG* 1.3 75.5 - - - +
173D TRP* 1.3 66.3 + - + +
174D ARG 3.2 2.2 - - - -
175D LEU* 3.4 30.4 - - + +
207D PHE* 3.7 35.2 - - + -
211D CYS* 4.7 12.6 - - - -
215D PHE* 5.7 1.3 - - + -
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Residues in contact with TRP 173 (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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139D ALA 5.5 0.7 - - - -
140D PHE* 3.2 70.6 - + + -
143D CYS* 4.4 19.1 - - + -
144D SER* 3.3 12.3 - - - +
169D MET 5.4 1.3 - - - -
170D LEU* 3.1 45.4 + - + +
172D LEU* 1.3 79.8 - - + +
174D ARG* 1.3 54.9 + - - +
175D LEU 3.1 7.8 + - - -
176D ARG* 3.8 8.4 + - - +
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Residues in contact with ARG 174 (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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70D VAL* 3.3 27.8 - - + +
73D SER* 3.3 32.3 + - - +
98D VAL* 3.9 18.8 + - - +
99D ASN* 3.4 20.6 + - - +
102D PHE* 3.7 46.0 - - + +
144D SER* 2.4 37.9 + - - -
145D THR* 4.4 0.8 - - - +
170D LEU 4.4 1.2 + - - -
171D ARG* 3.3 38.7 + - - +
173D TRP* 1.3 75.0 - - - +
175D LEU* 1.3 57.5 + - + +
176D ARG* 3.2 9.8 + - - +
177D ARG* 3.7 13.0 + - - +
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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