Contacts of the helix formed by residues 297 - 303 (chain B) in PDB entry 1UW9
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 MET 297 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A PHE* 4.4 16.6 - - + -
121A VAL* 3.4 26.5 - - + +
122A GLY 2.7 14.2 + - - -
274A PHE* 6.1 0.9 - - - -
301A ILE* 4.3 19.7 - - + -
309A ILE* 4.1 26.9 - - + -
314A LEU* 5.9 0.4 - - + -
1483A EDO 4.1 20.9 - - - -
270B LEU* 3.9 14.8 - - + +
271B THR* 3.9 22.0 - - + -
296B ALA* 1.3 73.4 - - - +
298B HIS* 1.3 64.9 + - - +
299B ALA 3.2 3.1 - - - -
300B VAL* 3.1 32.0 + - + +
301B ILE* 3.9 10.5 + - + +
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Residues in contact with HIS 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A GLY 5.1 4.0 - - - -
123A ASN* 6.0 1.6 - - - -
126A GLY* 5.7 2.5 - - - -
270B LEU* 3.7 17.9 - - + +
295B ARG* 2.9 77.1 + - + +
296B ALA* 3.3 1.4 + - - -
297B MET* 1.3 77.3 - - - +
299B ALA* 1.3 71.2 + - + +
301B ILE* 2.8 23.2 + - - +
302B ASP* 2.4 47.8 + - - +
311B PHE* 3.9 6.7 - - + -
314B LEU* 4.0 9.8 - - + +
335B LEU* 5.9 2.4 - - - +
1477B CAP 4.0 7.0 + - - -
1482B EDO 3.4 17.9 - - - -
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Residues in contact with ALA 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A GLY 5.5 2.2 + - - +
123A ASN 5.1 2.2 - - - +
125A PHE* 3.4 10.5 - - + +
126A GLY* 3.3 37.2 - - - +
307A HIS* 2.8 21.0 + - - -
297B MET 3.2 1.0 + - - -
298B HIS* 1.3 87.9 - - + +
300B VAL* 1.3 61.7 + - - +
301B ILE 3.0 1.7 + - - -
302B ASP* 3.2 14.6 - - - +
303B ARG* 3.3 14.5 + - + +
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Residues in contact with VAL 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A VAL* 3.8 24.5 - - + +
125A PHE* 3.7 31.6 - - + +
300A VAL 4.9 5.0 - - - +
301A ILE* 3.8 20.7 - - + +
307A HIS* 3.5 21.7 - - - -
308A GLY* 4.0 10.4 - - - -
309A ILE* 3.7 28.7 - - + -
297B MET* 3.1 23.3 + - + +
299B ALA* 1.3 77.8 - - - +
301B ILE* 1.3 58.0 + - - +
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Residues in contact with ILE 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A MET* 4.3 16.4 - - + -
300A VAL* 3.8 17.2 - - + +
301A ILE* 4.0 24.0 - - + -
307A HIS* 5.8 0.4 - - - -
1483A EDO 4.9 6.5 - - - -
270B LEU* 4.8 9.2 - - + -
297B MET* 4.2 25.8 - - + +
298B HIS 2.8 6.4 + - - +
300B VAL* 1.3 82.9 - - + +
302B ASP* 1.3 59.0 + - - +
303B ARG 3.7 1.1 - - - -
304B GLN 5.2 0.6 + - - -
307B HIS 3.9 4.9 - - - +
308B GLY* 3.3 10.2 - - - -
309B ILE* 3.1 48.6 + - + +
314B LEU* 4.1 18.4 - - + -
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Residues in contact with ASP 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B ARG* 3.0 23.2 + - - +
298B HIS* 2.4 43.9 + - - +
299B ALA* 3.2 15.4 + - - +
301B ILE* 1.3 77.5 - - - +
303B ARG* 1.3 64.8 + - - +
304B GLN 3.6 2.0 - - - -
309B ILE 3.0 23.1 - - - +
310B HIS* 4.0 0.4 - - - -
311B PHE* 3.3 33.4 + - - +
314B LEU* 4.1 3.8 - - + +
473B ASP* 4.1 8.1 - - - +
1482B EDO 4.2 7.0 + - - -
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Residues in contact with ARG 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A GLN* 4.5 0.8 - - - +
125A PHE 3.0 25.1 + - - +
126A GLY* 3.4 16.3 - - - -
127A PHE 2.9 25.2 + - - -
128A LYS* 4.0 6.5 + - - +
130A LEU* 2.9 30.7 + - - +
131A ARG 4.8 2.6 - - - +
307A HIS* 3.6 12.5 + - + +
299B ALA* 3.3 19.2 + - - +
301B ILE 3.7 1.2 - - - -
302B ASP* 1.3 83.3 + - - +
304B GLN* 1.3 75.1 + - - +
336B GLU* 2.9 45.0 + - - +
472B ILE* 3.6 22.4 - - + +
473B ASP* 3.4 22.4 - - - +
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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