Contacts of the strand formed by residues 151 - 156 (chain A) in PDB entry 4JHN
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 151 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A HIS* 3.1 13.4 + - - -
118A GLN* 4.5 0.2 - - - -
147A ALA* 3.3 0.9 - - - -
148A GLY* 3.0 41.5 + - - -
149A SER 3.2 11.1 + - - +
150A ASN* 1.3 85.1 - - - +
152A SER* 1.3 63.6 + - - +
164A TRP 3.6 5.2 - - - -
166A ASP* 3.5 23.1 - - + +
171A GLN* 3.5 21.1 - - + +
172A ILE* 3.9 12.1 - - + -
197A CYS* 3.8 11.4 - - - +
198A GLY 4.2 2.5 + - - +
199A TYR 5.0 1.6 - - - +
202A SER* 4.9 2.2 + - - +
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Residues in contact with SER 152 (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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98A HIS* 2.8 20.4 + - - -
100A LEU* 3.6 7.1 - - - +
118A GLN 2.6 22.2 + - - -
146A SER 3.5 6.1 - - - -
147A ALA* 4.4 0.2 - - - +
151A THR* 1.3 71.9 - - - +
153A ALA* 1.3 61.9 + - - +
163A MET* 3.2 9.2 - - - +
164A TRP* 3.0 63.8 + - - +
172A ILE* 4.5 0.2 - - - +
197A CYS* 4.3 2.7 - - - -
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Residues in contact with ALA 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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100A LEU* 3.9 2.3 - - - +
144A GLN 4.7 0.2 - - - -
145A LEU* 3.4 8.3 - - - +
146A SER* 2.8 36.3 + - - +
152A SER* 1.3 75.9 - - - +
154A ALA* 1.3 60.5 + - - +
155A LEU 4.4 0.2 - - - -
161A LEU* 4.2 2.5 - - + -
162A PHE 3.2 10.5 - - - +
163A MET* 3.9 8.5 - - + -
164A TRP* 4.1 4.5 - - - -
195A ILE* 3.9 23.6 - - + -
197A CYS* 3.7 19.7 - - - -
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Residues in contact with ALA 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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108A VAL* 5.6 0.2 - - + -
136A PHE* 3.7 33.0 - - + -
142A ILE* 4.4 11.2 - - + -
144A GLN 3.5 5.2 - - - +
145A LEU* 3.8 17.0 - - + -
153A ALA* 1.3 74.3 - - - +
155A LEU* 1.3 61.7 + - - +
160A ARG 3.8 1.2 - - - +
161A LEU* 3.7 3.3 - - - -
162A PHE* 2.8 35.5 + - - +
164A TRP* 3.8 5.1 - - + -
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Residues in contact with LEU 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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142A ILE* 3.6 3.8 - - - -
143A LYS* 2.7 43.2 + - + -
144A GLN* 2.8 33.3 + - + +
153A ALA 4.4 0.2 - - - -
154A ALA* 1.3 73.0 - - - +
156A THR* 1.3 63.7 + - - +
159A GLY 4.0 1.1 - - - -
160A ARG 3.5 18.2 - - - +
161A LEU* 4.2 4.5 - - + +
192A VAL* 3.4 38.1 - - + +
193A SER* 3.6 33.4 - - - +
194A TRP* 3.7 6.7 - - - +
195A ILE* 4.0 12.1 - - + -
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Residues in contact with THR 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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140A HIS* 4.0 27.1 - - + -
141A LYS 3.1 11.4 - - - +
142A ILE* 4.4 6.3 - - + -
143A LYS* 4.0 6.1 - - - +
154A ALA 5.3 0.2 - - - +
155A LEU* 1.3 83.9 - - - +
157A GLU* 1.3 63.4 + - - +
158A ASP* 2.6 27.6 + - - -
159A GLY* 3.0 14.0 + - - -
160A ARG* 2.9 39.2 + - - +
162A PHE* 4.0 19.1 - - + -
192A VAL 4.7 0.3 - - - +
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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