Contacts of the strand formed by residues 135 - 139 (chain A) in PDB entry 5HS6
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 135 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A TYR* 3.1 26.3 + - - -
84A ASP 2.9 9.1 + - - -
85A CYS* 3.2 12.0 - - - +
86A VAL 3.2 21.8 + - - -
129A LEU* 4.0 5.0 - - - +
134A GLY* 1.3 76.7 - - - +
136A VAL* 1.3 66.1 + - - +
137A ILE* 3.6 18.9 - - - +
177A VAL* 4.3 2.2 - - - -
178A ARG* 3.2 49.9 + - + +
180A ASN* 5.6 1.3 + - - +
231A LEU 4.1 1.0 - - - +
232A ALA* 3.5 20.7 + - - +
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Residues in contact with VAL 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A VAL* 3.5 7.9 - - + +
88A ASN* 4.0 12.3 - - - +
122A THR* 4.0 24.2 - - + +
126A LEU* 4.4 7.9 - - + -
129A LEU* 3.6 28.3 - - + -
135A ASN* 1.3 74.4 - - - +
137A ILE* 1.3 68.7 + - - +
138A ASN* 3.5 23.6 - - - +
177A VAL* 4.7 0.7 - - + -
178A ARG 2.9 7.1 + - - +
179A VAL* 3.5 27.7 - - + -
180A ASN* 2.9 27.2 + - - +
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Residues in contact with ILE 137 (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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29A PHE* 4.4 0.2 - - + -
85A CYS* 3.8 16.4 - - - -
86A VAL 2.9 11.6 + - - +
87A VAL* 3.2 13.2 - - + +
88A ASN 2.9 25.3 + - - -
135A ASN* 3.6 19.1 - - - +
136A VAL* 1.3 78.5 - - - +
138A ASN* 1.3 64.7 + - - +
139A ILE* 4.2 9.6 - - + -
180A ASN* 3.2 5.2 - - + +
182A ILE* 3.9 32.5 - - + +
228A ALA* 3.3 33.4 - - + +
231A LEU* 3.9 16.2 - - + -
232A ALA* 3.9 7.0 - - + +
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Residues in contact with ASN 138 (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 ASN* 3.0 31.6 + - - +
118A THR* 3.4 18.8 - - + +
122A THR* 5.3 0.8 + - - -
136A VAL* 3.5 14.2 - - - +
137A ILE* 1.3 74.0 - - - +
139A ILE* 1.3 63.5 + - - +
161A VAL* 3.8 18.7 + - + +
164A MET* 4.8 5.3 - - - +
165A THR* 3.0 39.2 + - - +
168A LEU* 5.8 2.0 - - - +
179A VAL* 4.4 3.4 - - - +
180A ASN 2.8 7.7 + - - -
181A CYS* 3.0 7.3 - - + +
182A ILE 2.8 25.8 + - - -
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Residues in contact with ILE 139 (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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21A ILE* 4.6 3.8 - - + -
25A ILE* 3.8 18.8 - - + -
87A VAL* 4.1 5.2 - - + -
88A ASN 2.9 24.5 + - - +
89A ASN* 3.8 28.7 - - + +
137A ILE* 4.2 7.9 - - + -
138A ASN* 1.3 73.0 - - - +
140A SER* 1.3 61.5 + - - +
158A LYS* 3.1 18.0 + - - -
161A VAL* 4.5 5.7 - - - +
182A ILE* 3.6 34.1 - - + -
184A PRO* 3.8 22.0 - - + -
224A VAL* 4.4 2.7 - - + -
301A NAD 3.6 25.2 + - - +
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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