Contacts of the strand formed by residues 179 - 185 (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 ASN 179 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ASN 5.2 0.6 - - - +
116A GLU* 3.1 37.2 + - - +
117A GLY* 4.8 0.9 - - - -
124A THR* 5.0 5.9 - - - +
165A GLY 3.2 17.9 - - - +
166A ASP* 4.0 4.5 - - - -
167A ASN* 4.0 5.8 - - - +
177A VAL* 3.4 4.7 - - - +
178A SER* 1.3 109.7 + - - +
180A VAL* 1.3 75.1 + - - +
181A CYS* 4.8 1.7 + - - +
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Residues in contact with VAL 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A GLU 3.6 3.7 - - - +
117A GLY 3.5 1.7 - - - +
163A MET 4.1 0.9 - - - +
164A TRP* 3.6 20.6 - - - +
165A GLY* 2.8 35.7 + - - -
172A ILE* 3.9 2.4 - - + +
174A LEU* 3.8 23.8 - - + -
177A VAL* 4.3 11.0 - - + -
179A ASN* 1.3 82.4 - - - +
181A CYS* 1.3 58.7 - - - +
182A VAL* 3.4 22.2 + - + +
184A GLN* 3.4 24.2 - - - +
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Residues in contact with CYS 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A GLY* 3.5 16.2 - - - -
120A GLY* 3.1 16.1 - - - -
122A GLY* 2.8 53.1 + - - -
123A ASP* 3.5 24.0 - - - +
124A THR* 5.1 4.7 - - + -
179A ASN* 4.8 2.6 + - - +
180A VAL* 1.3 73.6 - - - +
182A VAL* 1.3 62.7 + - - +
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Residues in contact with VAL 182 (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 GLY 4.4 1.6 - - - +
122A GLY* 3.9 16.2 - - - +
135A PHE* 4.2 16.6 - - + -
164A TRP* 3.9 3.4 - - - -
180A VAL* 3.4 20.0 - - + +
181A CYS* 1.3 91.7 - - - +
183A PRO* 1.4 86.5 - - + +
184A GLN* 3.4 4.3 + - - +
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Residues in contact with PRO 183 (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 GLY* 3.7 18.2 - - - +
133A ILE* 3.9 9.9 - - + -
135A PHE* 3.6 44.8 - - + -
136A PHE* 3.6 29.2 - - + -
162A PHE* 4.3 2.5 - - + -
164A TRP* 3.6 30.5 - - + -
182A VAL* 1.4 96.8 - - + +
184A GLN* 1.3 58.7 + - - +
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Residues in contact with GLN 184 (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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135A PHE* 5.4 0.4 - - - -
162A PHE* 3.8 4.9 - - - -
163A MET 2.9 36.2 + - - +
174A LEU* 3.8 26.0 - - + +
177A VAL* 5.6 4.4 - - - +
180A VAL* 3.4 29.1 - - - +
182A VAL 4.1 4.4 + - - +
183A PRO* 1.3 74.9 - - - +
185A GLN* 1.3 71.7 + - - +
186A VAL* 3.5 2.8 + - - +
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Residues in contact with GLN 185 (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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135A PHE* 5.8 0.2 - - - -
160A ARG* 3.8 33.4 - - - +
161A LEU 3.3 14.7 - - - +
162A PHE* 3.6 21.7 - - + -
174A LEU* 4.1 9.7 - - - +
184A GLN* 1.3 80.4 - - - +
186A VAL* 1.3 70.4 + - - +
187A THR* 4.1 22.8 + - + +
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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