Contacts of the helix formed by residues 165 - 175 (chain A) in PDB entry 4WMJ
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 165 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158A ASN* 4.4 6.0 + - - +
160A GLY 3.5 21.7 - - - +
161A ILE 4.2 2.7 - - - -
162A GLY 3.0 7.9 + - - +
163A GLY 3.2 0.4 - - - -
164A SER* 1.3 79.5 - - - +
166A LEU* 1.3 77.1 + - - +
167A GLY 3.2 2.4 + - - -
168A PRO* 3.3 4.9 - - - +
169A LEU* 2.9 35.4 + - - +
186A PHE* 3.7 25.5 - - - +
187A VAL 4.6 2.4 - - - +
188A SER* 3.6 25.9 + - - -
194A HIS* 5.5 0.7 - - - -
389B ASN* 6.2 0.2 - - - +
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Residues in contact with LEU 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 GLY* 2.9 13.8 + - - +
163A GLY* 5.5 0.2 - - - -
165A ASP* 1.3 84.7 + - - +
167A GLY* 1.3 58.4 + - - +
169A LEU* 4.5 11.9 - - + -
170A MET* 2.8 33.6 + - - +
350A ARG* 5.1 10.5 - - + +
353A ALA* 3.7 23.3 - - + +
354A TYR* 3.8 26.2 - - + +
357A GLN* 3.1 43.7 - - + +
389B ASN 6.0 0.2 - - - +
393B ALA* 4.3 12.3 - - + -
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Residues in contact with GLY 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 GLY* 4.6 5.5 + - - -
166A LEU* 1.3 76.2 - - - +
168A PRO* 1.3 73.6 - - - +
170A MET* 3.2 2.0 + - - +
171A VAL* 2.9 32.5 + - - +
279A LEU* 3.8 13.7 - - - -
354A TYR* 3.4 26.0 - - - -
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Residues in contact with PRO 168 (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 ASN* 4.9 2.0 - - - +
163A GLY 4.3 7.9 - - - +
164A SER 4.1 11.9 - - - +
165A ASP 3.3 14.6 - - - +
167A GLY* 1.3 87.2 - - - +
169A LEU* 1.3 58.3 + - - +
172A THR* 2.9 32.2 + - - +
186A PHE* 3.6 11.7 - - + -
279A LEU* 4.4 4.7 - - + -
283A ILE* 3.6 29.2 - - + +
284A GLY* 4.8 0.2 - - - -
286A SER* 3.4 23.1 - - - +
287A ILE* 3.9 18.3 - - + +
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Residues in contact with LEU 169 (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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165A ASP* 2.9 33.9 + - - +
166A LEU* 3.9 11.2 - - + +
168A PRO* 1.3 71.6 - - - +
170A MET* 1.3 68.3 + - - +
172A THR* 3.1 6.9 + - - -
173A GLU* 3.0 46.0 + - + +
186A PHE* 3.6 35.4 - - + -
350A ARG* 4.7 21.5 - - + +
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Residues in contact with MET 170 (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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166A LEU* 2.8 20.9 + - + +
167A GLY 3.9 0.4 - - - +
169A LEU* 1.3 80.0 - - - +
171A VAL* 1.3 68.0 + - + +
173A GLU* 3.6 2.7 - - - +
174A ALA* 2.9 29.7 + - - +
279A LEU* 5.1 0.2 - - + -
347A TYR 4.6 0.9 - - - +
348A LEU* 4.4 10.3 - - + -
350A ARG* 3.4 45.8 - - + +
351A PHE* 3.6 25.6 - - + +
354A TYR* 3.7 35.9 - - + -
490A LEU* 4.7 3.6 - - - -
494A ILE* 3.9 24.0 - - + -
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Residues in contact with VAL 171 (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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167A GLY 2.9 20.1 + - - +
170A MET* 1.3 80.0 - - + +
172A THR* 1.3 61.4 + - - +
174A ALA* 3.2 3.6 + - - -
175A LEU* 2.9 51.7 + - + +
279A LEU* 4.0 24.5 - - + -
287A ILE* 3.8 32.1 - - + -
299A LEU* 4.2 8.3 - - + -
490A LEU* 4.2 5.2 - - + -
494A ILE* 4.1 18.2 - - + -
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Residues in contact with THR 172 (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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168A PRO 2.9 22.6 + - - +
169A LEU 3.1 7.3 + - - -
171A VAL* 1.3 76.8 - - - +
173A GLU* 1.3 64.2 + - - +
175A LEU* 3.7 2.0 - - - +
176A LYS* 3.2 19.8 + - - +
184A VAL* 4.2 5.8 - - + +
186A PHE* 3.4 23.9 - - + -
286A SER 4.2 2.9 - - - +
287A ILE* 4.0 29.6 - - + -
290A TYR* 3.6 41.7 - - + -
291A ILE* 5.6 2.0 - - + -
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Residues in contact with GLU 173 (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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169A LEU* 3.0 39.1 + - + +
170A MET* 3.6 5.2 - - - +
172A THR* 1.3 83.1 + - - +
174A ALA* 1.3 61.3 + - - +
175A LEU 3.4 0.3 + - - -
176A LYS* 3.5 25.9 + - - +
184A VAL* 6.0 2.4 - - - +
186A PHE* 6.0 0.5 - - - -
290A TYR* 5.7 0.5 + - - -
347A TYR* 3.3 33.4 - - - +
349A HIS* 2.8 34.8 + - + +
350A ARG* 4.8 4.5 - - + -
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Residues in contact with ALA 174 (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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170A MET* 2.9 20.0 + - - +
171A VAL 3.2 4.7 + - - +
173A GLU* 1.3 76.1 - - - +
175A LEU* 1.3 64.1 + - + +
176A LYS 3.4 1.4 + - - -
177A PRO* 4.2 3.1 - - - +
178A TYR* 5.8 0.2 - - - -
345A ASP* 5.2 0.5 - - - +
347A TYR* 3.3 27.2 + - - +
348A LEU* 3.7 29.3 - - + +
416A HIS* 6.1 0.5 - - - -
485A PHE* 5.3 7.2 - - + +
490A LEU* 3.7 18.6 - - + -
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Residues in contact with LEU 175 (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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171A VAL* 2.9 33.5 + - + +
172A THR 3.7 2.9 - - - -
174A ALA* 1.3 84.1 - - + +
176A LYS* 1.3 57.5 + - - +
177A PRO* 3.2 5.6 - - - -
178A TYR* 2.8 37.7 + - + +
291A ILE* 3.6 37.8 - - + +
299A LEU* 4.6 4.9 - - + -
485A PHE* 4.6 5.4 - - + +
486A THR* 3.8 28.3 - - - +
487A PRO* 3.9 23.1 - - + -
490A LEU* 3.9 17.9 - - + -
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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