Contacts of the helix formed by residues 167 - 181 (chain A) in PDB entry 3JW8
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 THR 167 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A PRO* 3.3 23.3 - - - +
164A GLU* 3.9 10.1 - - - +
165A SER 3.9 0.6 - - - -
166A ALA* 1.3 79.7 - - - +
168A THR* 1.3 60.8 + - - +
169A PHE* 3.7 7.1 + - - +
170A LYS* 3.2 26.5 + - + +
171A VAL* 2.9 24.5 + - - +
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Residues in contact with THR 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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167A THR* 1.3 74.7 - - - +
169A PHE* 1.3 60.5 + - - +
171A VAL* 3.5 7.6 + - - +
172A LEU* 3.1 23.4 + - - +
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Residues in contact with PHE 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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167A THR* 3.2 6.5 + - - +
168A THR* 1.3 82.5 + - - +
170A LYS* 1.3 69.5 + - + +
172A LEU* 3.3 13.5 + - + +
173A ALA* 2.9 40.6 + - + +
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Residues in contact with LYS 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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164A GLU* 3.0 27.1 + - - +
165A SER* 3.4 23.6 - - - +
167A THR* 3.2 20.1 + - - +
169A PHE* 1.3 87.8 - - + +
171A VAL* 1.3 55.4 + - - +
173A ALA* 3.3 6.9 + - + +
174A ALA 2.9 17.5 + - - -
886A MRD 2.7 43.0 - - + +
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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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161A ALA* 5.3 2.0 - - + -
166A ALA* 3.7 26.9 - - + +
167A THR 2.9 21.4 + - - +
168A THR* 3.9 7.9 - - - +
169A PHE 3.2 0.4 - - - -
170A LYS* 1.3 72.5 - - - +
172A LEU* 1.4 64.7 - - - +
174A ALA* 3.2 7.6 + - - +
175A LYS* 3.1 49.7 + - - +
224A LEU* 4.0 26.7 - - + -
886A MRD 4.7 0.9 - - + -
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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 THR 3.1 15.2 + - - +
169A PHE* 3.7 17.5 - - + +
171A VAL* 1.4 75.5 - - - +
173A ALA* 1.3 58.3 + - - +
175A LYS* 3.2 16.9 + - + +
176A VAL* 2.9 45.9 + - + +
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Residues in contact with ALA 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 PHE* 2.9 30.5 + - + +
170A LYS* 3.4 14.6 - - + +
171A VAL 3.3 0.2 - - - -
172A LEU* 1.3 76.1 - - - +
174A ALA* 1.4 51.2 + - - +
176A VAL* 3.2 8.9 + - - +
177A LEU* 2.8 41.9 + - + +
886A MRD 4.8 7.4 - - + -
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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 LYS 2.9 19.4 + - - +
171A VAL 3.2 5.8 + - - +
173A ALA* 1.4 71.6 - - - +
175A LYS* 1.3 57.0 + - - +
177A LEU* 3.3 11.6 + - - +
178A ASN* 2.8 30.1 + - - +
217A VAL* 3.7 6.8 - - + +
221A ILE* 3.8 12.8 - - + -
224A LEU* 4.4 5.8 - - + -
886A MRD 3.8 35.8 - - + +
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Residues in contact with LYS 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* 3.1 39.0 + - + +
172A LEU* 3.6 18.8 - - + +
174A ALA* 1.3 73.7 - - - +
176A VAL* 1.3 64.9 + - - +
178A ASN* 3.4 4.1 + - - +
179A LEU* 3.3 25.6 + - - +
221A ILE* 3.9 19.5 - - + -
224A LEU* 5.5 6.3 - - + -
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Residues in contact with VAL 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* 2.9 32.4 + - + +
173A ALA* 3.5 10.5 - - - +
175A LYS* 1.3 76.5 - - + +
177A LEU* 1.4 65.7 + - + +
179A LEU* 3.1 22.6 + - + +
180A VAL* 3.4 19.2 + - + +
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Residues in contact with LEU 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 ALA* 2.8 27.1 + - + +
174A ALA* 3.3 11.2 + - - +
176A VAL* 1.4 76.0 - - + +
178A ASN* 1.3 57.0 + - - +
180A VAL* 4.6 4.9 - - + +
181A LEU* 2.7 52.0 + - + +
184A LEU* 4.2 22.7 - - + -
186A LEU* 4.9 6.3 - - + -
217A VAL* 3.8 24.9 - - + -
886A MRD 4.9 13.0 - - + -
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Residues in contact with ASN 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 ALA 2.8 17.0 + - - +
175A LYS* 3.5 8.0 + - - +
176A VAL 3.2 0.4 - - - -
177A LEU* 1.3 76.3 - - - +
179A LEU* 1.3 66.9 + - - +
182A PRO* 3.4 23.4 - - - +
217A VAL* 3.6 7.8 - - + +
218A CYS* 3.5 29.3 - - - +
221A ILE* 3.5 32.2 - - + +
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Residues in contact with LEU 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 LYS 3.6 14.4 - - - +
176A VAL* 3.1 13.9 + - + +
178A ASN* 1.3 86.0 - - - +
180A VAL* 1.3 65.3 + - + +
182A PRO* 4.5 3.1 - - - +
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Residues in contact with VAL 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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176A VAL* 3.4 20.4 + - + +
177A LEU* 3.2 6.3 + - + +
179A LEU* 1.3 86.0 - - + +
181A LEU* 1.3 84.4 + - + +
182A PRO* 3.7 5.7 - - - +
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Residues in contact with LEU 181 (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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177A LEU* 2.7 35.2 + - + +
180A VAL* 1.3 95.5 - - + +
182A PRO* 1.4 66.0 - - - +
183A ASN 3.1 3.6 - - - +
184A LEU* 3.1 40.1 + - + +
217A VAL* 3.9 5.5 - - - +
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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