Contacts of the strand formed by residues 137 - 140 (chain B) in PDB entry 1HYH
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 VAL 137 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ASP 3.3 6.8 + - - +
92B VAL* 3.3 7.8 - - + +
93B VAL 3.0 24.1 + - - -
134B PHE* 3.5 2.4 - - - -
136B GLY* 1.3 74.8 - - - +
138B LEU* 1.3 71.9 + - - +
139B VAL* 4.3 4.7 - - + -
162B LYS* 3.5 14.6 - - - +
164B ILE* 4.2 20.0 - - + -
263B VAL* 3.8 30.7 - - + -
292B ARG 3.6 14.4 - - - +
293B ASP* 4.1 2.2 - - - -
294B GLY* 3.5 33.4 - - - +
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Residues in contact with LEU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ILE* 5.0 0.9 - - + -
93B VAL* 3.4 34.1 - - + +
95B SER* 4.5 11.2 - - - -
129B LEU* 3.7 19.7 - - + -
134B PHE* 4.6 9.0 - - + -
136B GLY 4.0 1.0 + - - -
137B VAL* 1.3 72.8 - - - +
139B VAL* 1.4 64.5 + - - +
140B VAL* 4.0 11.4 - - + -
152B PHE* 3.9 39.3 - - + -
156B THR* 5.4 0.7 - - + -
158B PHE* 5.0 5.6 - - + -
162B LYS 2.9 15.1 + - - +
163B VAL* 3.6 18.3 - - + -
164B ILE* 3.0 29.8 + - - +
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Residues in contact with VAL 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B VAL* 4.0 20.0 - - + -
93B VAL 2.8 7.9 + - - +
94B ILE* 3.3 20.9 - - + +
95B SER* 2.8 32.6 + - - -
137B VAL* 4.3 9.9 - - + -
138B LEU* 1.4 75.8 - - - +
140B VAL* 1.3 58.6 + - - +
141B ILE* 5.1 0.2 - - + -
164B ILE* 3.3 8.7 - - + +
165B GLY 5.0 0.2 - - - -
166B THR* 4.2 25.1 - - + +
256B ALA* 4.7 9.4 - - + +
259B ILE* 3.8 34.1 - - + -
260B ALA* 5.1 2.7 - - - +
263B VAL* 5.5 0.4 - - + -
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Residues in contact with VAL 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B SER* 4.0 3.8 - - - +
138B LEU* 4.0 17.3 - - + +
139B VAL* 1.3 76.4 - - - +
141B ILE* 1.3 63.8 + - - +
142B SER* 4.1 14.8 - - - +
145B VAL* 3.3 4.6 - - + +
148B ILE* 4.0 16.2 - - + -
149B THR* 3.3 32.1 - - + +
152B PHE* 3.8 35.9 - - + -
163B VAL* 4.8 1.1 - - + -
164B ILE 2.8 16.5 + - - +
165B GLY* 3.2 2.8 - - - -
166B THR* 3.0 26.0 + - - -
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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
------------------------------------------------------------
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