Contacts of the strand formed by residues 90 - 94 (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 PHE 90 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B ILE* 3.4 15.5 - - + +
84B PHE* 3.0 40.1 + + + +
85B LEU* 4.0 13.9 - - + +
88B GLY* 4.1 2.9 - - - -
89B ILE* 1.3 75.1 + - + +
91B PHE* 1.3 59.6 + - - +
128B ILE* 3.9 8.1 - - + -
129B PRO* 4.0 15.7 - - + -
132B PHE* 3.3 61.0 - + + -
261B PRO* 4.6 1.8 - - + -
262B CYS 3.9 10.5 - - - -
288B LEU* 3.3 28.5 - - + -
289B HIS 3.2 18.6 - - - -
290B SER* 3.4 28.0 - - - -
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Residues in contact with PHE 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B TYR* 3.4 51.6 - + + -
56B LEU* 5.3 0.2 - - + -
57B ILE* 3.5 24.7 - - + -
64B LYS* 3.6 25.5 - - + +
65B ILE* 2.8 38.3 + - - -
88B GLY* 3.5 17.0 - - - +
89B ILE 3.7 2.2 - - - -
90B PHE* 1.3 73.6 - - - +
92B SER* 1.3 58.7 + - - +
264B ILE* 3.8 21.8 - - + -
289B HIS* 3.6 14.4 - - + -
290B SER 3.9 4.9 - - - -
291B THR* 3.5 37.0 - - + -
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Residues in contact with SER 92 (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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57B ILE* 4.3 2.2 - - - -
62B SER* 2.7 28.5 + - - -
63B SER 3.3 6.0 + - - -
65B ILE* 3.4 5.6 - - - +
91B PHE* 1.3 99.7 - - - +
93B HIS* 1.3 62.1 + - - +
264B ILE* 4.4 0.9 - - - -
288B LEU* 3.3 3.8 - - - -
289B HIS* 2.6 61.2 + - - +
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Residues in contact with HIS 93 (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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62B SER* 3.9 0.3 - - - -
63B SER* 2.7 72.6 + - - -
64B LYS 4.1 6.8 + - - -
65B ILE* 3.8 12.8 - - + -
69B LEU* 3.3 32.3 - - + +
92B SER* 1.3 78.8 + - - +
94B ARG* 1.3 66.0 + - - +
95B ASP* 4.1 6.1 - - - -
96B MET* 3.2 27.8 + - + +
97B ASN* 4.6 8.5 - - + -
287B LEU 3.1 16.4 - - - +
288B LEU* 3.8 15.3 - - + -
289B HIS* 4.5 2.0 - - - -
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Residues in contact with ARG 94 (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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60B PHE 2.9 27.3 + - - -
61B GLY 4.0 4.8 + - - -
62B SER* 3.8 19.0 - - - +
63B SER* 4.5 1.3 - - - -
93B HIS* 1.3 81.5 - - - +
95B ASP* 1.3 70.2 + - - +
96B MET 3.1 2.1 + - - -
267B ASP* 2.6 44.5 + - - -
271B ARG* 3.8 22.0 - - - +
274B ARG* 3.5 37.5 - - - +
286B ALA* 3.3 3.1 - - - +
287B LEU* 3.0 48.0 + - + +
289B HIS* 4.2 4.3 - - + -
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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