Contacts of the helix formed by residues 164 - 180 (chain A) in PDB entry 4WGK
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 SER 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A MET 3.8 2.2 + - - -
163A VAL* 1.3 75.5 - - - +
165A GLN* 1.3 64.2 + - - +
166A ARG 3.8 3.1 + - - -
167A LEU* 3.1 22.8 + - - +
168A ARG* 3.0 19.2 + - - +
202A TYR* 2.7 25.3 + - - -
203A PHE* 3.4 37.2 - - - -
204A GLN 5.3 0.4 - - - -
574A ASN 3.2 8.9 - - - +
575A VAL* 4.5 0.9 - - - +
576A TYR 4.7 2.2 - - - +
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Residues in contact with GLN 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A SER* 1.3 72.7 - - - +
166A ARG* 1.3 57.8 - - - +
168A ARG* 3.3 4.0 + - - +
169A LEU* 3.0 47.6 + - + +
204A GLN* 3.6 16.6 - - - +
205A TYR* 3.8 30.7 + - + +
429A TRP* 6.1 0.2 - - - -
521A ILE 3.0 27.5 + - - -
523A ASP* 3.2 21.9 + - - +
574A ASN 3.7 8.1 + - - +
575A VAL* 3.9 22.9 - - + +
576A TYR 4.9 0.2 - - - +
631A PRO* 3.6 27.0 - - + +
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Residues in contact with ARG 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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164A SER* 3.2 7.0 + - - +
165A GLN* 1.3 79.0 - - - +
167A LEU* 1.3 62.9 + - - +
169A LEU* 4.0 1.4 - - - +
170A GLU* 3.1 24.3 + - - +
202A TYR 4.5 1.6 - - - +
203A PHE 4.6 2.9 - - - -
204A GLN* 3.9 45.2 + - + +
215A PHE* 3.8 39.7 - - - -
220A PHE* 3.8 16.5 - - + -
633A PHE* 3.6 36.1 - - + -
634A PHE 2.6 28.7 + - - -
635A LYS* 3.9 12.6 + - - +
636A GLN 6.2 0.2 - - - -
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Residues in contact with LEU 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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158A ILE* 4.9 1.3 - - + -
160A ILE* 4.3 23.1 - - + -
163A VAL* 4.4 20.4 - - + -
164A SER* 3.1 27.1 + - - +
166A ARG* 1.3 77.9 - - - +
168A ARG* 1.3 63.0 + - - +
170A GLU* 3.8 1.2 - - - +
171A VAL* 3.0 29.6 + - + +
190A LEU* 5.6 1.6 - - + -
202A TYR* 4.8 3.1 - - + +
220A PHE* 3.8 18.3 - - + -
223A MET* 4.2 17.7 - - + -
224A VAL* 3.7 27.6 - - + -
227A ILE* 3.8 26.5 - - + -
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Residues in contact with ARG 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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163A VAL* 4.6 1.7 - - + +
164A SER 3.0 6.7 + - - +
165A GLN* 3.8 4.9 - - - +
167A LEU* 1.3 77.0 - - - +
169A LEU* 1.3 63.3 + - + +
171A VAL* 3.4 1.6 + - - +
172A LEU* 2.9 53.9 + - + +
185A ARG* 2.5 44.7 + - - +
188A VAL 2.9 21.2 + - - -
190A LEU* 3.9 25.1 - - + +
427A HIS* 3.8 13.7 + - - -
429A TRP* 5.7 0.2 - - - +
523A ASP* 3.7 17.9 + - - -
525A GLN* 3.9 0.8 + - - -
574A ASN* 2.9 61.9 + - - +
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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 GLN* 3.0 38.1 + - + +
166A ARG 4.0 0.7 - - - +
168A ARG* 1.3 79.8 - - + +
170A GLU* 1.3 61.6 + - - +
172A LEU* 3.5 13.9 + - + +
173A ASN* 3.0 36.4 + - - +
204A GLN* 4.9 0.9 - - - +
429A TRP* 5.3 9.0 - - + +
631A PRO* 4.3 23.6 - - + +
632A PRO 3.7 26.5 - - - +
633A PHE* 3.9 25.1 - - + -
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Residues in contact with GLU 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 ARG 3.1 19.3 + - - +
167A LEU 3.8 2.9 - - - +
169A LEU* 1.3 76.9 - - - +
171A VAL* 1.3 63.7 + - - +
173A ASN* 3.3 12.2 + - - +
174A ARG* 2.8 69.0 + - - +
220A PHE* 3.8 27.4 - - + -
221A GLN* 5.6 0.7 - - - -
224A VAL* 4.1 7.2 - - + -
633A PHE* 3.4 25.0 - - + -
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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 LEU* 3.0 24.1 + - + +
168A ARG 3.7 3.4 - - - +
170A GLU* 1.3 75.7 - - - +
172A LEU* 1.3 59.2 + - + +
174A ARG* 3.3 4.0 + - - +
175A LEU* 2.9 46.3 + - + +
190A LEU* 4.0 21.1 - - + -
224A VAL* 4.2 25.4 - - + +
227A ILE* 4.1 41.1 - - + -
228A LEU* 4.0 7.9 - - + +
231A ILE* 4.8 0.7 - - + -
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Residues in contact with LEU 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 ARG* 2.9 58.7 + - + +
169A LEU* 3.9 13.2 - - + +
171A VAL* 1.3 78.4 - - + +
173A ASN* 1.3 64.5 + - - +
175A LEU* 3.4 19.9 + - + +
176A GLN* 3.1 22.7 + - - +
183A TYR 4.9 2.5 - - - +
184A ARG* 3.7 29.2 - - - +
185A ARG* 4.1 12.8 - - + +
188A VAL* 4.3 12.1 - - + -
190A LEU* 5.7 0.9 - - + -
429A TRP* 6.3 1.8 - - + -
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Residues in contact with ASN 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 26.8 + - - +
170A GLU* 3.6 16.5 + - - +
171A VAL 3.3 0.2 - - - -
172A LEU* 1.3 77.7 - - - +
174A ARG* 1.3 60.7 + - + +
176A GLN* 3.3 13.3 + - - +
177A SER* 3.1 28.6 + - - -
633A PHE* 5.1 7.1 - - - -
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Residues in contact with ARG 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 GLU* 2.8 41.9 + - - +
171A VAL 3.8 2.0 - - - +
173A ASN* 1.3 74.7 - - + +
175A LEU* 1.3 65.3 + - - +
177A SER* 3.4 10.2 + - - -
178A LYS* 3.2 23.9 + - - +
221A GLN* 2.7 35.8 + - - +
224A VAL* 3.3 26.4 - - - +
225A THR* 4.2 14.8 - - - +
228A LEU* 3.6 30.9 - - + +
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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 37.1 + - + +
172A LEU* 3.6 21.8 - - + +
173A ASN 3.3 0.2 - - - -
174A ARG* 1.3 77.2 - - - +
176A GLN* 1.3 52.2 + - - +
178A LYS 3.4 0.2 + - - -
179A TYR* 2.8 65.0 + - + +
180A GLY 4.6 0.2 - - - +
183A TYR* 4.2 28.9 - - + +
188A VAL* 4.4 8.7 - - + -
228A LEU* 3.7 20.6 - - + -
231A ILE* 4.0 28.7 - - + -
232A ASP* 5.4 0.2 - - - +
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Residues in contact with GLN 176 (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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172A LEU 3.1 14.1 + - - +
173A ASN* 3.5 14.5 - - - +
174A ARG 3.3 0.2 - - - -
175A LEU* 1.3 74.3 - - - +
177A SER* 1.3 62.9 + - - +
180A GLY* 2.8 47.1 + - - +
183A TYR 4.7 3.3 + - - +
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Residues in contact with SER 177 (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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173A ASN 3.1 15.6 + - - -
174A ARG* 3.6 12.9 - - - -
176A GLN* 1.3 78.6 - - - +
178A LYS* 1.3 58.6 + - - +
180A GLY 4.9 0.3 + - - -
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Residues in contact with LYS 178 (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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174A ARG 3.2 13.3 + - - +
177A SER* 1.3 81.6 - - - +
179A TYR* 1.3 98.0 + - + +
180A GLY 3.7 0.7 - - - -
232A ASP* 3.5 23.8 + - - +
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Residues in contact with TYR 179 (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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175A LEU* 2.8 41.6 + - + +
178A LYS* 1.3 102.6 - - + +
180A GLY* 1.3 62.2 + - - +
181A SER 3.2 3.3 + - - -
182A LEU* 3.3 25.2 + - + +
183A TYR* 3.5 36.6 - + + +
228A LEU* 6.0 0.4 - - + -
231A ILE* 4.7 2.2 - - + -
232A ASP* 2.2 47.6 + - - +
235A HIS* 3.6 41.3 - + + +
236A THR* 5.6 0.5 - - - +
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Residues in contact with GLY 180 (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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175A LEU 4.6 0.2 - - - +
176A GLN* 2.8 42.4 + - - +
177A SER 4.9 0.2 + - - -
178A LYS 3.7 0.8 - - - -
179A TYR* 1.3 76.1 - - - +
181A SER* 1.3 61.2 + - - -
182A LEU 3.3 1.2 + - - -
183A TYR 4.3 8.0 + - - +
184A ARG* 5.2 0.9 - - - +
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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