Contacts of the helix formed by residues 167 - 174 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B PHE* 4.4 40.7 - - + -
163B GLY* 3.6 22.4 - - - +
164B PHE* 3.8 13.8 + - + +
165B ARG 3.2 0.8 - - - -
166B ILE* 1.3 81.0 - - + +
168B SER* 1.3 58.4 + - - +
169B MET 3.2 1.3 - - - -
170B LEU* 3.4 47.0 + - + +
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Residues in contact with SER 168 (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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77B CYS* 3.3 19.4 + - - -
80B GLN* 4.4 5.5 + - - -
148B PHE* 5.3 1.8 - - - +
149B GLN* 4.8 19.1 - - - +
164B PHE 4.1 2.1 + - - -
165B ARG* 3.2 21.7 + - - -
166B ILE 3.1 1.4 - - - -
167B LEU* 1.3 75.2 - - - +
169B MET* 1.3 57.2 + - - +
170B LEU 3.2 5.6 + - - -
171B ARG* 3.2 34.9 + - - +
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Residues in contact with MET 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B CYS* 3.3 36.3 - - - +
78B PRO* 3.7 5.6 - - + -
81B PHE* 3.6 30.7 - - + -
165B ARG 4.6 1.6 - - - +
166B ILE* 2.9 27.8 + - + +
168B SER* 1.3 75.0 - - - +
170B LEU* 1.3 59.1 + - + +
171B ARG 3.1 5.4 - - - -
172B LEU* 3.1 40.8 + - + +
173B TRP* 4.4 2.1 + - - -
215B PHE* 3.6 30.1 - - + -
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Residues in contact with LEU 170 (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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143B CYS* 3.5 32.3 - - + +
144B SER* 3.1 23.6 + - - -
148B PHE* 5.0 7.9 - - + -
166B ILE 5.3 2.2 - - - +
167B LEU* 3.4 41.5 - - + +
168B SER 3.2 1.2 - - - -
169B MET* 1.3 77.3 - - + +
171B ARG* 1.3 55.6 + - - +
172B LEU 3.1 5.4 - - - -
173B TRP* 3.1 49.2 + - + +
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Residues in contact with ARG 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B TYR* 5.7 0.4 - - - -
73B SER* 3.5 32.8 + - - +
74B ALA* 5.4 0.5 - - - +
76B ILE* 3.6 32.7 - - - +
77B CYS* 3.6 30.0 + - - +
80B GLN* 3.4 19.6 - - - +
95B ASP* 4.4 17.1 + - - +
98B VAL* 6.1 2.0 - - - +
99B ASN* 5.4 9.9 - - - +
144B SER* 4.3 5.2 - - - +
168B SER* 3.2 31.3 + - - +
169B MET 3.1 1.2 - - - -
170B LEU* 1.3 76.3 - - - +
172B LEU* 1.3 56.8 + - - +
173B TRP 3.3 1.1 - - - -
174B ARG* 3.3 48.9 - - - +
175B LEU* 5.8 0.2 - - - +
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Residues in contact with LEU 172 (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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74B ALA* 3.8 28.3 - - + +
77B CYS* 4.0 17.9 - - + -
78B PRO* 4.9 3.1 - - + -
169B MET* 3.1 30.9 + - + +
170B LEU 3.1 1.2 - - - -
171B ARG* 1.3 74.5 - - - +
173B TRP* 1.3 66.5 + - + +
174B ARG 3.2 2.9 - - - -
175B LEU* 3.4 28.8 - - + +
207B PHE* 3.7 36.1 - - + -
211B CYS* 4.7 12.6 - - - -
215B PHE* 5.7 0.7 - - + -
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Residues in contact with TRP 173 (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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139B ALA 5.5 0.4 - - - -
140B PHE* 3.2 69.7 - + + -
143B CYS* 4.4 18.6 - - + -
144B SER* 3.3 12.1 - - - +
169B MET 5.4 1.3 - - - -
170B LEU* 3.1 44.9 + - + +
172B LEU* 1.3 80.4 - - + +
174B ARG* 1.3 55.6 + - - +
175B LEU* 3.1 8.4 + - - -
176B ARG* 3.8 8.3 + - - +
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Residues in contact with ARG 174 (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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70B VAL* 3.3 27.9 - - + +
73B SER* 3.3 31.8 + - - +
98B VAL* 3.9 18.4 + - - +
99B ASN* 3.4 20.4 + - - +
102B PHE* 3.7 46.2 - - + +
144B SER* 2.4 38.4 + - - -
145B THR* 4.4 0.8 - - - +
170B LEU 4.4 1.0 + - - -
171B ARG* 3.3 37.4 + - - +
173B TRP* 1.3 75.2 - - - +
175B LEU* 1.3 58.0 + - + +
176B ARG* 3.2 10.1 + - - +
177B ARG* 3.7 13.2 + - - +
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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