Contacts of the strand formed by residues 135 - 139 (chain A) in PDB entry 2HUE
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 ILE 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A LYS* 3.7 6.8 - - - +
18A PHE* 3.0 45.0 + - + +
89A LEU* 4.1 20.6 - - + -
90A VAL* 3.7 24.7 - - + -
115A ASN* 3.8 31.9 - - + +
116A GLU 3.7 6.7 - - - +
117A TYR* 3.8 14.1 - - + +
130A VAL* 5.2 0.7 - - + -
131A GLN 3.8 10.8 - - - +
132A VAL* 3.1 29.9 + - + +
133A ASP 3.4 2.1 - - - +
134A HIS* 1.3 77.9 - - - +
136A VAL* 1.3 65.7 + - - +
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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
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15A PRO* 4.1 15.3 - - + -
16A ALA 3.5 13.7 - - - +
17A LYS* 5.4 3.8 - - + -
114A ASN 3.8 0.5 - - - +
115A ASN* 3.4 1.9 - - - -
116A GLU* 2.8 40.1 + - + +
118A ASP* 3.6 33.2 - - + +
135A ILE* 1.3 77.7 - - - +
137A ARG* 1.3 69.8 + - - +
138A ASN* 5.6 1.7 - - + +
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Residues in contact with ARG 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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13A ASN* 3.8 7.1 + - - +
14A ASN* 4.0 1.6 + - - +
15A PRO* 3.2 6.9 - - - +
16A ALA* 2.7 59.9 + - - +
17A LYS 3.2 17.5 + - - +
18A PHE* 3.3 20.7 + - + +
20A ASP 2.8 20.2 + - - -
21A PRO 3.0 29.5 + - - -
22A TYR* 3.4 47.4 + - - +
113A VAL* 4.0 11.2 - - + -
114A ASN 3.2 5.8 - - - +
115A ASN* 3.4 18.8 - - - +
135A ILE 4.2 0.8 + - - -
136A VAL* 1.3 74.6 - - - +
138A ASN* 1.3 62.3 + - - +
139A ILE* 4.4 9.7 - - + +
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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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14A ASN* 3.6 9.9 - - - +
15A PRO* 4.4 18.1 - - + +
113A VAL* 3.5 1.0 - - - +
114A ASN* 2.8 28.6 + - + +
136A VAL* 5.6 1.3 - - + -
137A ARG* 1.3 78.6 - - - +
139A ILE* 1.3 77.1 + - - +
113B HIS* 2.8 38.6 + - - +
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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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11A VAL* 4.0 24.7 - - + -
13A ASN 5.4 2.2 - - - +
14A ASN* 2.8 43.5 + - + +
22A TYR* 3.9 31.6 - - + -
24A PHE* 4.6 3.4 - - + -
95A ILE* 4.0 9.2 - - + -
111A TYR* 3.7 36.6 - - + -
112A TYR 3.5 4.5 - - - +
113A VAL* 4.0 18.2 - - + +
137A ARG* 4.4 8.7 - - - +
138A ASN* 1.3 80.2 + - - +
140A LEU* 1.3 62.1 + - - +
141A ALA* 2.8 10.3 + - - +
142A GLU* 5.5 0.2 - - - +
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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