Contacts of the helix formed by residues 160 - 170 (chain J) in PDB entry 4PHZ
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 160 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240I ILE* 5.3 13.7 - - + -
243I THR* 4.2 26.0 - - + -
131J VAL* 4.3 19.5 - - + -
132J PRO* 4.4 7.6 - - + -
135J TRP* 4.0 33.9 - - + -
156J GLY* 2.9 28.6 + - - +
157J TRP 4.3 3.4 - - - +
159J LEU* 1.3 78.8 - - + +
161J PHE* 1.3 67.9 + - - +
162J TYR 3.5 0.2 - - - -
163J PRO* 3.6 9.2 - - + -
164J ASN* 3.1 22.9 + - - +
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Residues in contact with PHE 161 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65J TRP* 3.7 35.0 - + - -
66J PRO* 3.8 32.1 - - + +
69J VAL* 3.4 30.3 - - + -
70J PRO* 3.9 19.7 - - + -
127J SER* 3.8 5.8 - - - -
128J ALA 3.9 7.0 - - - -
129J LEU* 3.8 18.8 - - + -
132J PRO* 4.4 4.7 - - + -
157J TRP* 3.7 8.5 + + - +
158J GLY 3.2 12.9 + - - +
159J LEU 3.2 3.0 - - - -
160J LEU* 1.3 77.4 - - - +
162J TYR* 1.3 69.2 + - - +
164J ASN* 2.7 23.8 + - - +
165J ASN* 3.1 33.8 + - - -
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Residues in contact with TYR 162 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247I TYR* 5.9 3.1 - + - -
60J LYS 4.9 0.3 + - - -
61J ASP 3.6 19.0 + - - -
62J ARG* 4.0 13.9 - - - +
65J TRP* 3.4 31.1 - + - -
66J PRO* 3.9 24.7 - - + +
158J GLY 4.7 0.6 + - - -
159J LEU 4.1 1.2 + - - +
161J PHE* 1.3 81.3 - + - +
163J PRO* 1.3 65.3 - - + +
165J ASN* 3.1 4.4 + - - +
166J TRP* 2.8 63.8 + + + +
169J ILE* 4.5 5.3 - - + +
173J HIS* 4.6 8.3 - - - -
218J VAL* 3.6 41.1 - - + -
222J ALA* 5.8 4.2 - - + +
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Residues in contact with PRO 163 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187I TRP* 5.2 0.2 - - - -
243I THR* 4.3 18.2 - - + +
247I TYR* 4.1 28.8 - - + +
159J LEU 3.1 23.1 - - - +
160J LEU* 3.6 11.2 - - + +
162J TYR* 1.3 92.7 - - + +
164J ASN* 1.3 61.4 + - - +
166J TRP* 3.0 13.7 + - - +
167J PRO* 3.1 13.7 - - - +
222J ALA* 6.2 0.4 - - + -
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Residues in contact with ASN 164 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187I TRP* 2.6 39.0 + - + +
191I TRP* 5.7 1.6 - - - -
243I THR* 4.4 7.7 - - + +
128J ALA* 2.8 41.4 + - - +
130J ILE 4.5 0.3 + - - -
131J VAL* 3.7 33.8 + - + +
132J PRO* 3.7 17.7 - - - +
160J LEU 3.1 17.4 + - - +
161J PHE* 2.7 25.9 + - - +
163J PRO* 1.3 77.1 - - - +
165J ASN* 1.3 54.4 + - - +
167J PRO* 4.3 0.2 - - - -
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Residues in contact with ASN 165 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187I TRP* 4.9 0.2 - - - +
188I HIS* 5.0 1.9 + - - -
60J LYS* 5.5 0.3 - - - +
65J TRP* 3.5 32.7 - - + -
125J PHE* 5.8 1.6 - - - -
126J PRO 4.8 0.9 - - - +
127J SER* 3.6 2.4 - - - -
128J ALA* 2.8 44.0 + - - +
161J PHE* 3.1 44.5 + - - +
162J TYR* 3.5 5.4 - - - +
163J PRO 3.1 1.0 - - - -
164J ASN* 1.3 74.8 - - - +
166J TRP* 1.3 67.3 + - - +
167J PRO* 3.4 2.9 - - - -
168J ALA* 2.9 20.4 + - - +
169J ILE* 3.1 14.8 + - + +
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Residues in contact with TRP 166 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247I TYR* 3.4 39.2 - + + -
250I THR* 3.6 19.5 + - - -
251I ASN* 3.4 22.6 + - - +
254I PHE 5.3 4.0 - - - -
257I THR* 3.7 29.4 - - + -
162J TYR* 2.8 41.3 + + + +
163J PRO 3.4 7.2 - - - +
165J ASN* 1.3 71.5 - - - +
167J PRO* 1.4 59.8 - - + +
169J ILE* 2.7 41.4 + - + -
170J ALA* 2.7 58.9 + - + +
173J HIS* 4.5 12.3 - + + -
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Residues in contact with PRO 167 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183I ARG* 3.9 24.1 - - - +
187I TRP* 3.7 44.6 - - + -
243I THR 5.6 0.4 - - - +
246I GLY 3.6 24.9 - - - +
247I TYR* 4.3 2.5 - - - +
250I THR* 3.4 27.6 - - + +
163J PRO 3.1 15.0 - - - +
164J ASN 4.3 2.0 - - - -
165J ASN 3.5 2.2 - - - -
166J TRP* 1.4 93.7 - - + +
168J ALA* 1.3 60.2 + - - +
169J ILE 3.6 0.2 + - - -
170J ALA* 4.4 3.5 + - - +
171J ALA 5.1 0.5 + - - -
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Residues in contact with ALA 168 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183I ARG* 5.4 1.2 - - - +
184I VAL* 4.0 16.3 - - - +
187I TRP* 4.3 11.8 - - + -
188I HIS* 4.1 29.8 - - + +
125J PHE* 3.8 16.4 - - + -
165J ASN* 2.9 14.7 + - - +
167J PRO* 1.3 80.2 - - - +
169J ILE* 1.3 60.2 + - + +
171J ALA* 5.0 2.1 + - - +
172J PHE* 3.4 23.6 - - - -
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Residues in contact with ILE 169 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57J VAL* 4.5 8.7 - - + -
60J LYS* 3.8 33.7 - - + +
65J TRP* 4.6 14.4 - - + -
125J PHE* 3.2 42.0 - - + -
162J TYR* 4.5 9.4 - - + +
165J ASN* 3.1 9.3 + - - +
166J TRP* 2.7 42.2 + - + +
168J ALA* 1.3 78.4 - - + +
170J ALA* 1.3 62.3 + - - +
171J ALA 3.3 2.5 - - - -
172J PHE* 2.9 19.7 + - - +
173J HIS* 3.7 20.0 + - + +
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Residues in contact with ALA 170 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250I THR* 4.4 9.0 - - - +
254I PHE* 4.1 20.8 - - + -
257I THR* 3.5 15.3 - - + +
166J TRP* 2.7 60.3 + - + +
167J PRO 4.4 1.5 + - - +
168J ALA 3.8 0.4 - - - -
169J ILE* 1.3 72.7 - - - +
171J ALA* 1.3 63.8 + - - +
173J HIS 2.9 12.2 + - - +
174J GLN* 3.7 1.4 + - - +
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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