Contacts of the helix formed by residues 156 - 167 (chain A) in PDB entry 3ORY
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 GLU 156 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ASP* 3.4 7.9 - - - +
91A LYS* 4.1 15.7 - - - +
153A ALA* 3.9 0.2 - - - +
155A ALA* 1.3 83.4 - - - +
157A GLY* 1.3 64.6 + - - +
158A GLU* 4.3 2.5 - - + +
159A ALA* 3.5 21.9 - - + +
160A GLN* 3.1 21.7 + - - +
183A PHE* 3.9 17.7 - - + -
240A ASP* 4.2 9.0 - - - +
241A TYR* 2.6 36.2 + - - -
286A TYR* 2.6 35.2 + - - -
291A GLN 4.8 2.5 + - - +
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Residues in contact with GLY 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ASP* 3.1 15.5 - - - -
82A VAL* 3.6 11.0 - - - +
83A PHE 4.6 0.4 - - - -
84A ASP* 3.0 27.5 + - - -
153A ALA* 4.1 13.0 - - - -
155A ALA 3.3 1.6 + - - -
156A GLU* 1.3 71.2 - - - +
158A GLU* 1.3 55.1 + - - +
160A GLN* 3.3 1.9 + - - +
161A ALA* 2.9 29.1 + - - +
354A PO4 5.4 0.9 + - - -
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Residues in contact with GLU 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ASP* 3.0 25.0 + - - +
156A GLU* 3.2 2.1 - - + +
157A GLY* 1.3 76.3 - - - +
159A ALA* 1.3 56.5 + - - +
161A ALA* 3.5 4.5 + - - +
162A ALA* 3.1 23.2 + - - +
173A SER* 5.5 0.9 - - - -
174A ALA 5.1 0.3 - - - +
175A SER* 2.7 30.1 + - - -
177A ASP* 2.9 10.5 - - - +
179A ASP* 3.6 26.5 - - + +
180A SER* 3.5 32.0 + - - +
183A PHE* 3.8 8.1 - - + -
354A PO4 2.5 37.4 + - - +
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Residues in contact with ALA 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A GLU* 3.2 22.4 + - + +
158A GLU* 1.3 75.7 - - - +
160A GLN* 1.3 59.3 + - - +
162A ALA* 3.4 3.6 + - - +
163A TYR* 3.0 23.6 + - - +
183A PHE* 3.4 37.7 - - + +
290A PRO* 3.8 18.6 - - + +
291A GLN 4.8 1.3 - - - +
292A VAL* 3.4 14.3 - - + +
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Residues in contact with GLN 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A VAL* 3.7 18.4 - - + -
151A VAL* 4.1 6.4 - - + +
153A ALA* 3.5 26.5 - - + -
154A PRO* 3.5 6.3 - - + +
156A GLU 3.1 4.0 + - - +
157A GLY 3.7 0.9 - - - +
159A ALA* 1.3 74.4 - - - +
161A ALA* 1.3 66.0 + - - +
163A TYR* 3.2 5.5 + - - +
164A ILE* 2.9 42.8 + - + +
291A GLN 5.8 0.4 - - - +
292A VAL* 3.3 14.4 - - + +
293A THR* 2.8 54.2 + - - +
296A TYR* 3.5 21.8 - - - -
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Residues in contact with ALA 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A VAL* 3.6 24.8 - - + +
31A ASP* 5.2 3.4 - - + +
82A VAL* 3.8 15.0 - - + +
157A GLY 2.9 17.8 + - - +
158A GLU* 3.6 11.7 - - - +
160A GLN* 1.3 76.6 - - - +
162A ALA* 1.3 63.0 + - - +
164A ILE* 3.3 0.9 + - - +
165A VAL* 3.2 25.3 + - - +
173A SER* 3.9 20.6 - - - -
180A SER* 4.8 1.1 - - - -
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Residues in contact with ALA 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A GLU 3.1 12.4 + - - +
159A ALA 3.5 7.0 - - - +
160A GLN 3.3 0.2 - - - -
161A ALA* 1.3 74.3 - - - +
163A TYR* 1.3 57.8 + - - +
165A VAL* 3.3 4.7 + - - +
166A LYS* 2.9 31.9 + - - +
180A SER* 3.3 28.2 - - - +
183A PHE* 3.5 16.8 - - + +
185A SER* 3.4 24.2 - - - +
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Residues in contact with TYR 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A ALA 3.0 16.5 + - - +
160A GLN* 3.2 8.9 + - - +
162A ALA* 1.3 74.3 - - - +
164A ILE* 1.3 60.2 + - - +
166A LYS* 3.2 24.5 + - + +
167A LYS* 2.9 65.1 + - + +
292A VAL* 3.6 34.3 - - + -
293A THR 3.4 24.7 - - - -
294A ASP* 2.6 36.9 + - - -
296A TYR* 4.5 3.1 - + - -
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Residues in contact with ILE 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A VAL* 3.9 23.8 - - + -
82A VAL* 4.9 0.9 - - + -
151A VAL* 4.2 23.8 - - + -
160A GLN* 2.9 44.8 + - + +
161A ALA* 3.3 6.9 + - - +
163A TYR* 1.3 75.6 - - - +
165A VAL* 1.3 61.4 + - - +
167A LYS* 3.4 4.5 + - - +
169A ASP* 2.9 45.6 + - + +
170A ALA* 3.7 22.0 - - + -
296A TYR* 3.8 18.6 - - + -
298A ILE* 4.0 11.7 - - + -
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Residues in contact with VAL 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A VAL* 3.8 7.9 - - + -
161A ALA 3.2 14.6 + - - +
162A ALA 3.6 6.1 - - - +
163A TYR 3.2 0.2 - - - -
164A ILE* 1.3 74.3 - - - +
166A LYS* 1.3 64.2 + - - +
168A GLY* 3.0 15.1 + - - -
170A ALA* 3.6 12.7 - - + +
171A TYR 3.5 21.3 - - - +
172A ALA* 3.4 32.3 - - - +
173A SER* 3.5 4.7 - - - +
185A SER* 3.9 7.4 - - - +
186A PRO* 3.6 30.0 - - + +
187A LYS 4.4 1.1 - - - +
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Residues in contact with LYS 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A ALA 2.9 18.8 + - - +
163A TYR* 3.3 29.3 - - + +
165A VAL* 1.3 75.5 - - - +
167A LYS* 1.3 62.9 + - + +
168A GLY* 3.1 1.3 + - - -
183A PHE 3.4 22.5 + - - -
184A GLY* 3.4 29.9 - - - +
186A PRO* 4.0 11.2 - - + +
288A LEU 4.8 11.9 + - - -
290A PRO* 5.3 5.1 - - - +
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Residues in contact with LYS 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A TYR* 2.9 62.4 + - + +
164A ILE 3.8 2.0 - - - +
165A VAL 3.2 0.6 - - - -
166A LYS* 1.3 77.5 - - + +
168A GLY* 1.3 59.8 + - - +
169A ASP* 3.6 11.5 + - - +
294A ASP* 3.8 10.0 - - - +
296A TYR* 3.6 20.6 - - - +
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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