Contacts of the strand formed by residues 130 - 133 (chain A) in PDB entry 1HS6
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 TYR 130 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A PHE* 3.6 6.6 - - - -
116A GLN 3.9 0.9 - - - +
118A LEU* 3.1 37.0 + - + +
123A THR* 3.8 14.4 - - + -
129A PRO* 1.3 80.0 - - - +
131A LEU* 1.3 82.9 + - - +
132A PHE* 4.1 10.5 - + + -
205A VAL* 3.5 30.6 - - + +
206A VAL 3.2 7.9 - - - -
207A GLY* 4.3 10.1 - - - -
208A ALA 4.8 0.9 - - - -
209A LEU* 3.8 25.4 - - + +
222A SER* 5.5 0.2 - - - -
223A GLU* 4.2 28.3 - - + -
259A LEU* 3.9 10.7 - - - +
260A VAL 4.2 2.6 + - - -
261A LEU* 4.0 5.5 - - - +
262A PRO* 3.6 41.5 - - + +
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Residues in contact with LEU 131 (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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27A VAL* 3.7 26.7 - - + -
29A PHE* 3.6 17.5 - - + -
34A LEU* 5.0 4.9 - - + -
115A LEU* 4.0 25.4 - - + -
116A GLN 3.7 10.3 - - - +
117A TRP* 3.6 33.0 - - + -
130A TYR* 1.3 79.8 - - - +
132A PHE* 1.3 66.9 - - - +
204A LEU* 4.3 18.4 - - + +
205A VAL* 3.2 7.3 - - - +
206A VAL* 2.6 48.0 + - + +
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Residues in contact with PHE 132 (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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114A ALA 3.8 0.2 - - - +
115A LEU* 3.6 7.4 - - - +
116A GLN* 3.3 61.7 + - + -
118A LEU* 4.7 3.8 - - + -
130A TYR* 4.1 10.1 - + + -
131A LEU* 1.3 76.7 - - - +
133A SER* 1.3 69.4 + - - +
134A GLN* 5.0 0.4 - - + -
204A LEU 3.4 8.5 - - - +
205A VAL* 4.5 4.3 - - + -
261A LEU* 3.3 31.9 - - + -
262A PRO* 4.0 22.7 - - + -
264A SER* 4.0 7.6 - - - -
265A PHE* 3.7 34.1 - + - -
266A PRO* 4.0 0.2 - - + -
277A PHE* 4.6 1.1 - - + -
596A HIS* 3.7 24.7 - + - -
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Residues in contact with SER 133 (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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114A ALA 3.1 6.7 - - - -
115A LEU* 3.5 18.4 - - - -
132A PHE* 1.3 79.9 - - - +
134A GLN* 1.3 66.8 + - - +
135A CYS* 4.7 1.1 - - - -
143A ILE* 4.1 15.3 - - - -
202A ILE 4.1 2.4 + - - -
203A ALA* 3.4 12.5 - - - +
204A LEU* 2.8 39.5 + - - -
272A ASN* 5.4 0.3 - - - +
277A PHE* 3.6 19.2 - - - -
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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