Contacts of the strand formed by residues 257 - 263 (chain B) in PDB entry 1ULH
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 GLN 257 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95B ASP* 5.1 1.6 + - - +
98B GLN* 3.8 27.1 + - - +
99B VAL* 3.7 27.4 - - + -
102B ALA* 5.2 7.8 - - + +
108B PRO 4.1 7.1 + - - +
109B PHE* 3.2 17.2 - - + -
110B TYR* 3.0 26.3 + - - -
255B ASP 3.0 7.8 + - - +
256B ILE* 1.3 76.7 - - - +
258B CYS* 1.3 81.4 + - - +
283B PRO* 5.0 11.7 - - - +
284B LYS 3.6 18.2 + - - -
286B ALA* 3.7 12.9 - - - +
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Residues in contact with CYS 258 (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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109B PHE* 5.2 0.2 - - - -
110B TYR* 3.7 27.8 - - + -
112B TYR* 3.9 14.1 - - - -
241B SER* 3.5 29.4 - - - +
256B ILE 3.5 1.5 + - - +
257B GLN* 1.3 88.1 + - - +
259B LEU* 1.3 59.6 + - - +
260B ILE* 3.9 22.9 - - - -
283B PRO* 5.7 2.3 + - - +
284B LYS 5.1 1.0 + - - -
285B PRO* 4.1 11.1 - - + +
286B ALA* 2.6 30.9 + - - +
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Residues in contact with LEU 259 (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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96B MET* 3.9 23.3 - - + -
99B VAL* 4.2 7.2 - - + -
109B PHE* 3.5 32.5 - - + -
110B TYR 3.0 13.3 + - - +
111B LEU* 3.3 19.2 - - + -
112B TYR 3.0 23.2 + - - -
136B LEU* 4.6 5.6 - - + -
258B CYS* 1.3 74.7 - - - +
260B ILE* 1.3 67.0 + - - +
261B PRO* 3.7 2.3 - - + +
286B ALA* 3.5 22.0 - - + -
287B LEU 4.1 1.8 - - - +
288B LEU* 3.5 38.6 - - + -
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Residues in contact with ILE 260 (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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112B TYR* 3.1 41.1 - - + +
113B THR* 4.6 3.4 - - - -
241B SER* 3.7 9.2 - - - +
258B CYS* 3.9 6.7 - - - -
259B LEU* 1.3 78.0 - - - +
261B PRO* 1.3 70.4 - - - +
262B CYS* 3.7 2.4 + - + -
270B PHE* 3.5 51.6 - - + -
285B PRO* 3.7 18.2 - - + -
286B ALA 2.8 11.6 + - - +
287B LEU* 3.4 16.7 - - + +
288B LEU 3.1 20.4 + - - -
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Residues in contact with PRO 261 (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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90B PHE* 4.6 2.2 - - + -
111B LEU* 3.9 23.3 - - + -
112B TYR 3.3 17.3 - - - +
113B THR* 2.7 32.3 + - - -
129B PRO* 4.7 5.4 - - - +
132B PHE* 4.5 18.2 - - + -
133B THR* 3.5 24.2 + - + +
136B LEU* 4.5 8.1 - - + -
259B LEU* 3.7 9.2 - - + +
260B ILE* 1.3 81.4 - - - +
262B CYS* 1.3 63.6 + - - +
288B LEU* 3.5 13.0 - - + +
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Residues in contact with CYS 262 (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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90B PHE* 3.9 3.9 - - - -
113B THR* 4.8 2.2 - - - +
129B PRO* 4.5 8.7 - - - -
260B ILE* 4.3 5.2 - - + -
261B PRO* 1.3 76.8 - - - +
263B ALA* 1.3 73.8 + - - +
266B GLN* 4.0 25.1 - - + -
270B PHE* 4.3 7.9 - - + -
287B LEU* 4.0 25.8 - - - -
288B LEU 2.9 12.8 + - - +
289B HIS* 3.1 13.5 - - - -
290B SER* 2.9 22.5 + - - -
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Residues in contact with ALA 263 (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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129B PRO* 4.7 10.6 - - + +
262B CYS* 1.3 84.0 - - - +
264B ILE* 1.3 58.5 + - - +
265B ASP* 2.8 29.7 + - - +
266B GLN* 3.2 8.1 + - + +
290B SER* 3.3 23.5 + - - +
291B THR 4.6 1.8 - - - +
292B PHE* 4.0 17.0 - - + -
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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
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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