Contacts of the strand formed by residues 144 - 149 (chain A) in PDB entry 1JHH
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 VAL 144 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A MET* 4.2 14.1 - - + -
123A ILE* 4.0 23.6 - - + -
125A ILE* 4.7 7.9 - - + -
143A GLN* 1.3 72.0 - - - +
145A VAL* 1.3 59.9 + - - +
155A VAL* 3.8 27.6 - - + -
156A LYS 3.6 7.2 - - - +
157A ARG* 4.2 19.3 - - - +
191A LEU* 3.6 8.2 - - - +
192A ALA* 3.1 40.4 + - + +
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Residues in contact with VAL 145 (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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139A VAL* 4.0 33.9 - - + -
143A GLN* 3.8 14.8 - - + +
144A VAL* 1.3 79.2 - - - +
146A VAL* 1.3 68.0 + - - +
147A ALA* 3.9 7.6 + - + -
154A THR 3.7 0.5 - - - +
155A VAL* 3.4 7.6 - - - +
156A LYS 3.0 38.2 + - - +
158A LEU* 4.4 17.7 - - + -
167A LEU* 5.0 3.8 - - + -
188A ILE* 4.0 21.5 - - + -
190A GLY 3.4 13.9 - - - +
191A LEU* 4.5 1.1 - - + -
192A ALA* 4.6 0.7 - - - +
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Residues in contact with VAL 146 (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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88A LEU* 4.7 4.5 - - + -
113A LEU* 3.7 15.7 - - + -
131A LEU* 3.9 27.4 - - + -
133A VAL* 3.9 24.2 - - + -
145A VAL* 1.3 73.3 - - - +
147A ALA* 1.3 55.6 + - - +
153A VAL* 3.7 26.7 - - + -
154A THR 3.5 4.9 - - - +
155A VAL* 4.4 3.1 - - + -
188A ILE* 3.7 2.9 - - - +
189A GLU* 2.7 45.8 + - + -
190A GLY 3.0 17.9 + - - +
192A ALA 5.2 2.9 - - - +
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Residues in contact with ALA 147 (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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145A VAL* 3.8 8.2 - - + -
146A VAL* 1.3 75.2 - - - +
148A ARG* 1.3 61.3 + - - +
149A ILE* 3.8 8.9 - - + +
152A GLU 3.7 0.7 - - - +
153A VAL* 3.3 4.1 - - - +
154A THR* 2.9 38.4 + - + +
167A LEU* 4.7 4.5 - - + -
186A PHE* 3.6 33.0 - - + -
187A THR 3.4 7.2 - - - +
188A ILE* 4.3 6.7 - - + -
189A GLU* 4.4 3.4 - - - +
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Residues in contact with ARG 148 (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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82A VAL* 3.3 15.2 - - - +
83A ALA 2.7 31.9 + - - -
86A GLU 2.7 26.2 + - - +
87A PRO* 3.9 2.0 - - - +
88A LEU* 3.6 17.4 - - - +
147A ALA* 1.3 72.1 - - - +
149A ILE* 1.3 63.0 + - - +
150A ASP 4.0 0.2 - - - -
151A ASP* 3.4 41.0 + - - +
152A GLU 3.2 11.4 - - - +
153A VAL* 4.1 11.0 - - + +
185A SER 3.6 1.4 - - - +
186A PHE* 3.3 8.5 - - - -
187A THR* 2.9 42.5 + - - +
189A GLU* 3.5 22.1 + - + +
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Residues in contact with ILE 149 (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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147A ALA* 3.8 10.1 - - + +
148A ARG* 1.3 77.3 - - - +
150A ASP* 1.3 73.1 + - - +
151A ASP 3.2 0.2 - - - -
152A GLU* 2.7 36.2 + - + +
154A THR* 3.5 31.9 - - + -
167A LEU* 3.8 10.5 - - + -
177A ILE* 5.2 7.9 - - + -
179A VAL* 3.8 29.6 - - + -
184A GLN* 3.5 25.8 - - - +
185A SER 3.5 7.6 - - - +
186A PHE* 4.0 4.0 - - + -
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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