Contacts of the helix formed by residues 151 - 163 (chain L) in PDB entry 1JH0
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 TRP 151 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62L GLN* 3.3 49.4 + - + +
150L ILE* 1.3 96.3 - - + +
152L THR* 1.3 62.2 + - + +
153L HIS 3.0 2.5 - - - -
154L LEU* 2.7 39.8 + - + +
155L ASP* 3.0 17.6 + - - +
853L BCL 4.3 18.2 - - - -
197M PHE* 3.3 26.5 - - + -
198M TYR* 4.5 28.5 - + + -
200M PRO* 6.1 4.5 - - + -
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Residues in contact with THR 152 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62L GLN 5.9 2.5 - - - +
63L LEU 4.8 5.2 - - - +
64L ILE 4.6 1.8 - - - +
65L SER* 2.9 36.5 + - - +
67L TYR* 3.2 25.9 + - + +
147L PRO* 3.4 13.2 - - - +
149L GLY* 3.1 17.0 + - - -
151L TRP* 1.3 79.9 - - + +
153L HIS* 1.3 61.7 + - - +
155L ASP* 3.4 16.3 + - - +
156L TRP 3.2 16.3 + - - -
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Residues in contact with HIS 153 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146L PHE* 4.2 6.5 - + + -
147L PRO* 3.1 31.9 - - + +
149L GLY 2.7 20.9 + - - +
150L ILE* 3.0 22.6 + - - -
151L TRP 3.0 1.4 - - - -
152L THR* 1.3 80.0 + - - +
154L LEU* 1.3 80.9 + - + +
156L TRP* 3.4 4.7 + - - +
157L VAL* 3.2 24.6 + - - +
853L BCL 2.8 68.0 + + + -
855L BPH 3.5 23.5 - - + +
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Residues in contact with LEU 154 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150L ILE 3.9 12.1 - - - +
151L TRP* 2.7 20.3 + - + +
153L HIS* 1.3 97.2 + - + +
155L ASP* 1.3 70.5 + - - +
157L VAL* 3.1 7.2 + - - +
158L SER 2.9 17.7 + - - -
853L BCL 3.6 59.0 - - + +
197M PHE* 3.4 50.6 - - + +
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Residues in contact with ASP 155 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67L TYR* 5.4 1.4 + - - +
151L TRP* 3.0 16.5 + - - +
152L THR* 3.5 20.1 - - - +
154L LEU* 1.3 77.6 - - - +
156L TRP* 1.3 55.3 + - - +
158L SER* 2.7 10.6 + - - -
159L ASN* 2.6 49.7 + - - +
195M ASN* 5.9 1.2 + - - -
197M PHE* 5.9 1.0 - - - -
198M TYR* 3.9 18.6 + - - -
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Residues in contact with TRP 156 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131L LEU* 4.5 14.4 - - + -
135L ARG* 4.2 9.0 - - - -
143L GLY 5.0 1.7 + - - -
144L TYR 3.1 21.3 + - - -
145L ALA* 3.0 25.5 + - - -
146L PHE* 3.3 31.0 - + + -
147L PRO* 3.5 20.4 - - + -
152L THR 3.2 4.1 + - - +
153L HIS 3.4 8.3 - - - +
155L ASP* 1.3 79.6 - - - +
157L VAL* 1.3 77.5 + - + +
159L ASN* 4.1 7.7 - - - +
160L THR* 2.5 54.4 + - + -
248L MET* 4.0 21.5 - - + -
851L BCL 4.0 17.0 - - + -
853L BCL 4.4 8.7 - - + -
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Residues in contact with VAL 157 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153L HIS 3.2 15.9 - - - +
154L LEU* 3.1 9.4 + - + +
155L ASP 3.0 0.8 - - - -
156L TRP* 1.3 95.9 - - + +
158L SER* 1.3 59.1 + - - +
160L THR* 3.6 1.2 - - - -
161L GLY* 2.8 29.6 + - - -
851L BCL 3.7 28.0 - - + +
853L BCL 3.8 33.0 - - + -
197M PHE* 4.1 7.6 - - + -
852M BCL 3.6 26.7 - - + +
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Residues in contact with SER 158 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154L LEU 2.9 12.6 + - - -
155L ASP* 2.7 16.9 + - - -
157L VAL* 1.3 73.4 - - - +
159L ASN* 1.3 61.4 + - - -
161L GLY* 4.1 0.2 - - - -
162L TYR* 3.1 48.0 + - - +
851L BCL 4.1 9.4 - - - +
195M ASN* 3.8 17.8 + - - -
197M PHE* 3.7 20.1 - - - -
852M BCL 5.6 0.5 - - - +
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Residues in contact with ASN 159 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155L ASP* 2.6 37.0 + - - +
156L TRP* 4.1 5.4 - - - +
158L SER* 1.3 71.5 + - - +
160L THR* 1.3 63.6 + - - +
161L GLY 3.1 0.2 - - - -
162L TYR* 3.5 3.6 + - - +
163L THR* 2.8 29.0 + - - +
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Residues in contact with THR 160 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135L ARG* 4.0 24.7 - - - +
156L TRP* 2.5 54.1 + - + -
157L VAL 3.7 2.7 - - - -
159L ASN* 1.3 73.9 - - - +
161L GLY* 1.3 62.2 + - - +
163L THR* 3.6 5.6 - - - -
164L TYR* 3.2 26.6 - - + -
167L PHE* 4.7 1.0 - - + -
248L MET* 4.2 10.3 - - + -
251L THR* 5.5 0.4 - - + -
851L BCL 3.8 17.0 - - + -
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Residues in contact with GLY 161 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157L VAL 2.8 15.6 + - - -
158L SER 4.1 0.9 - - - -
160L THR* 1.3 75.4 - - - +
162L TYR* 1.3 57.9 + - - +
163L THR 3.0 9.3 + - - -
164L TYR 3.2 8.3 + - - -
165L GLY 3.0 12.8 + - - +
167L PHE* 3.9 23.1 - - - -
851L BCL 4.0 26.2 - - - +
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Residues in contact with TYR 162 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158L SER* 3.1 36.0 + - - +
159L ASN* 3.9 3.6 - - - +
161L GLY* 1.3 72.4 - - - +
163L THR* 1.3 63.2 + - - +
164L TYR 3.1 0.7 - - - -
165L GLY* 3.1 30.3 + - - -
166L ASN* 4.9 4.7 - - - -
167L PHE 5.7 0.4 - - - -
258L GLN* 5.2 0.5 + - - -
851L BCL 3.7 23.3 - - + -
187M ASN* 2.6 36.9 + - - -
190M SER* 4.6 3.1 + - - -
191M LEU* 3.2 29.2 - - + +
195M ASN* 5.9 1.8 - - - -
852M BCL 3.6 10.3 - - + +
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Residues in contact with THR 163 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159L ASN 2.8 21.6 + - - -
160L THR* 3.6 13.8 + - - -
161L GLY 3.0 1.0 + - - -
162L TYR* 1.3 78.2 - - - +
164L TYR* 1.3 85.7 + - + +
165L GLY 3.3 1.6 + - - -
257L ASP 5.8 0.2 - - - -
258L GLN* 3.6 10.9 + - - -
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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