Contacts of the strand formed by residues 152 - 161 (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 GLU 152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A ALA 3.7 0.3 - - - +
148A ARG* 3.2 1.6 - - - -
149A ILE* 2.7 55.8 + - + +
150A ASP 3.1 5.5 + - - +
151A ASP* 1.3 74.3 - - + +
153A VAL* 1.3 64.0 + - - +
154A THR* 5.4 0.9 - - - -
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Residues in contact with VAL 153 (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* 4.2 16.2 - - + -
88A LEU* 3.8 25.6 - - + -
113A LEU* 4.3 13.9 - - + -
146A VAL* 3.7 27.8 - - + -
147A ALA 3.3 4.5 - - - +
148A ARG* 4.1 24.5 - - + +
151A ASP 3.7 1.3 + - - +
152A GLU* 1.3 78.3 - - - +
154A THR* 1.3 69.1 + - - +
155A VAL* 5.6 0.7 - - + -
189A GLU* 5.5 0.9 - - + -
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Residues in contact with THR 154 (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 3.7 0.7 - - - +
146A VAL* 3.5 4.0 - - - +
147A ALA* 2.9 35.4 + - + +
149A ILE* 3.5 28.3 - - + -
152A GLU* 5.4 0.7 - - - -
153A VAL* 1.3 79.6 - - - +
155A VAL* 1.3 63.3 + - - +
156A LYS* 2.6 45.3 + - + +
167A LEU* 4.1 10.3 - - + -
177A ILE* 4.5 9.1 - - + +
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Residues in contact with VAL 155 (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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113A LEU* 4.6 11.9 - - + -
115A VAL* 4.8 20.0 - - + -
119A ALA* 5.0 0.3 - - - +
120A MET* 3.4 23.7 - - + +
125A ILE* 5.0 6.1 - - + -
131A LEU* 3.9 32.1 - - + -
144A VAL* 3.8 24.2 - - + -
145A VAL 3.4 6.5 - - - +
146A VAL* 4.4 9.2 - - + -
153A VAL* 5.6 0.4 - - + -
154A THR* 1.3 79.3 + - - +
156A LYS* 1.3 77.6 + - - +
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Residues in contact with LYS 156 (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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119A ALA* 3.7 24.8 - - - +
120A MET* 4.0 11.9 - - - -
144A VAL* 4.3 1.3 - - - -
145A VAL* 3.0 33.6 + - - +
154A THR* 2.6 38.2 + - + +
155A VAL* 1.3 85.7 + - - +
157A ARG* 1.3 62.9 + - - +
158A LEU 3.7 0.7 + - - -
167A LEU* 3.7 33.7 - - + +
168A LEU 3.5 16.8 - - - +
169A PRO* 4.0 15.9 - - + -
174A PHE* 5.2 4.0 - - - -
175A LYS 5.7 1.6 - - - -
177A ILE* 4.2 19.9 - - + +
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Residues in contact with ARG 157 (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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120A MET* 4.0 6.7 - - + +
123A ILE* 4.0 22.4 - - - +
142A GLY* 2.6 51.4 + - - +
143A GLN* 3.5 6.3 - - - +
144A VAL* 4.2 13.5 - - + +
156A LYS* 1.3 71.7 - - - +
158A LEU* 1.3 64.8 + - - +
166A GLU 3.7 0.2 - - - +
167A LEU* 3.5 6.0 - - - -
168A LEU* 2.8 63.1 + - + +
170A GLU* 2.9 33.2 + - + +
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Residues in contact with LEU 158 (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 24.9 - - + -
140A ARG* 3.9 24.0 - - - +
141A ASN* 3.6 11.1 - - - +
142A GLY* 2.8 28.6 + - - -
143A GLN 3.0 17.1 + - - +
145A VAL* 4.4 9.2 - - + -
156A LYS 3.7 1.0 + - - -
157A ARG* 1.3 73.2 - - - +
159A LYS* 1.3 62.0 + - - +
160A LYS* 4.1 15.7 - - + +
165A VAL* 3.5 32.1 - - + -
166A GLU 4.1 0.9 - - - -
167A LEU* 4.2 10.5 - - + -
168A LEU* 5.4 0.8 - - - +
186A PHE* 4.4 10.5 - - + -
188A ILE* 4.7 7.0 - - + -
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Residues in contact with LYS 159 (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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141A ASN* 3.7 6.5 - - - +
158A LEU* 1.3 76.6 - - - +
160A LYS* 1.3 72.2 + - - +
161A GLN* 3.6 24.9 + - + +
165A VAL* 4.6 1.1 - - - -
166A GLU* 2.9 65.8 + - + +
168A LEU* 3.8 25.5 - - + +
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Residues in contact with LYS 160 (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 4.8 10.3 + - - -
140A ARG* 5.1 2.0 - - - +
141A ASN* 2.9 48.3 - - - +
158A LEU* 4.3 19.7 - - + -
159A LYS* 1.3 78.3 - - - +
161A GLN* 1.3 69.0 + - - +
162A GLY 4.0 4.0 - - - +
164A LYS 4.2 4.0 - - - +
165A VAL* 4.6 9.9 - - + +
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Residues in contact with GLN 161 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159A LYS* 3.6 31.5 + - + +
160A LYS* 1.3 83.3 - - - +
162A GLY* 1.3 59.7 + - - +
163A ASN 3.2 0.9 + - - -
164A LYS* 2.8 41.0 + - + +
166A GLU* 3.9 31.3 + - + +
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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