Contacts of the strand formed by residues 144 - 148 (chain A) 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 LEU 144 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A LEU* 3.4 23.6 - - + +
112A TYR* 3.9 3.1 - - - +
113A THR* 4.3 7.9 - - + -
133A THR* 3.4 28.7 - - + -
137A GLN* 3.4 20.0 - - + +
143A PRO* 1.3 78.4 - - - +
145A VAL* 1.3 80.5 + - - +
146A ILE* 3.9 12.1 - - + -
180A PHE* 3.5 40.4 - - + -
184A LYS 2.9 4.7 + - - +
185A THR* 3.5 11.3 - - + -
186A PHE* 3.2 22.9 + - - +
419A LEU* 4.7 1.4 - - - +
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Residues in contact with VAL 145 (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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110A TYR* 4.6 10.1 - - + -
111A LEU 3.0 11.5 + - - +
112A TYR* 3.4 21.4 - - + -
113A THR 3.1 23.2 + - - +
143A PRO* 6.1 0.4 - - + -
144A LEU* 1.3 80.9 - - - +
146A ILE* 1.3 59.2 + - - +
186A PHE* 3.4 17.3 - - + -
188A PHE* 3.4 20.4 - - + -
246A PHE* 3.5 41.1 - - + -
249A ILE* 4.2 9.2 - - + -
250A PHE* 4.9 4.0 - - + -
419A LEU* 6.1 0.2 - - + -
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Residues in contact with ILE 146 (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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113A THR* 3.2 13.0 - - + +
114A GLY* 4.4 1.3 - - - -
130A PHE* 4.1 21.5 - - + -
144A LEU* 3.9 17.3 - - + -
145A VAL* 1.3 77.1 - - - +
147A GLN* 1.3 65.6 + - - +
148A MET* 4.2 7.6 - - - -
175A ILE* 3.5 39.7 - - + -
180A PHE* 4.0 13.2 - - + -
185A THR* 3.8 16.6 - - + -
186A PHE 2.8 10.7 + - - -
187A ILE* 3.3 23.6 - - + +
188A PHE* 2.9 31.5 + - - +
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Residues in contact with GLN 147 (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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112A TYR* 3.7 27.2 + - + -
113A THR 2.9 8.5 + - - -
114A GLY* 3.1 4.7 - - - -
115A ARG 2.6 33.1 + - - +
145A VAL 4.0 0.6 + - - -
146A ILE* 1.3 73.8 - - - +
148A MET* 1.3 62.8 + - - +
149A THR* 3.0 26.5 + - + +
188A PHE* 3.4 21.8 - - + -
190A ASP* 2.9 28.1 + - - +
200A PHE* 4.2 1.2 - - - -
236A ILE* 3.6 6.9 + - - +
237A GLN* 3.9 21.0 + - - +
240A PRO* 3.3 23.4 - - - +
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Residues in contact with MET 148 (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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115A ARG* 3.4 36.3 - - + +
117A PRO* 4.0 6.7 - - + -
146A ILE* 4.2 3.8 - - - -
147A GLN* 1.3 80.2 - - - +
149A THR* 1.3 62.2 + - - +
150A ASP* 3.1 14.1 - - - +
168A ALA* 3.9 32.1 - - + +
171A ASN* 3.7 21.5 - - + -
172A ALA* 4.5 1.1 - - - +
175A ILE* 3.7 21.3 - - + -
187A ILE* 3.7 24.9 - - + -
188A PHE 3.0 18.1 + - - +
189A SER* 4.3 3.1 - - - -
190A ASP* 3.2 15.2 + - - -
414A MET* 5.5 2.7 - - + -
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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