Contacts of the strand formed by residues 105 - 109 (chain A) in PDB entry 2UYO
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 105 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ILE* 3.5 4.2 - - - +
104A ARG* 1.3 80.7 - - - +
106A PHE* 1.3 63.3 + - - +
127A THR* 3.6 14.2 + - - +
129A TYR* 4.0 12.9 + - + -
174A GLY 4.6 0.6 + - - -
175A PHE* 3.3 26.8 - - + +
176A ASP* 2.9 50.3 + - - +
179A ALA* 3.7 12.7 - - + +
180A ARG 3.5 10.3 + - - +
181A THR* 2.8 23.4 + - - +
182A ALA 2.9 23.9 + - - -
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Residues in contact with PHE 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A PHE* 3.7 29.2 - + + -
98A ALA* 3.7 11.7 - - + -
99A VAL* 3.6 20.9 - - + -
103A ILE* 3.4 33.2 - - + -
104A ARG 3.7 5.6 - - - -
105A GLN* 1.3 76.6 - - - +
107A VAL* 1.4 63.5 + - - +
108A ILE 4.2 0.2 - - - -
122A TRP* 3.7 16.8 - + + -
126A THR* 3.5 31.0 - - + -
127A THR 2.9 7.9 + - - +
128A VAL* 3.5 14.3 - - + -
129A TYR* 2.8 31.8 + - - -
182A ALA* 3.3 31.9 - - + +
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Residues in contact with VAL 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A PHE* 4.4 0.6 - - - -
106A PHE* 1.4 79.7 - - - +
108A ILE* 1.3 63.8 + - - +
109A LEU* 3.9 7.4 - - + +
129A TYR* 3.4 12.3 - - + +
131A ILE* 3.8 28.5 - - + -
170A LEU* 4.4 1.6 - - + -
175A PHE* 3.7 35.2 - - + -
181A THR* 3.8 8.7 - - + -
182A ALA 2.9 9.1 + - - +
183A TRP* 3.4 32.4 - - + +
184A LEU* 2.8 28.6 + - - +
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Residues in contact with ILE 108 (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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95A PHE* 3.7 31.4 - - + -
107A VAL* 1.3 73.2 - - - +
109A LEU* 1.3 63.4 + - - +
110A ALA 3.8 0.2 + - - -
111A SER* 3.5 27.5 - - - -
114A ASP* 3.6 28.9 - - + +
116A ARG* 4.2 14.4 - - + +
117A ALA 4.6 4.5 - - - +
128A VAL* 4.1 20.0 - - + -
129A TYR 2.8 14.5 + - - +
130A GLU* 3.7 12.6 - - + -
131A ILE* 3.0 26.0 + - - +
184A LEU* 3.9 11.7 - - + +
186A GLU* 6.5 0.7 - - + -
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Residues in contact with LEU 109 (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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107A VAL* 3.9 9.2 - - + +
108A ILE* 1.3 72.8 - - - +
110A ALA* 1.3 74.3 + - - +
111A SER* 4.2 1.0 - - - -
131A ILE* 3.7 29.4 - - + -
162A LEU* 3.9 16.8 - - + -
166A TRP* 4.6 5.4 - - + -
183A TRP* 4.1 21.3 - - + -
184A LEU 2.9 24.5 + - - +
185A ALA* 4.1 19.0 - - + -
186A GLU 4.6 5.4 + - - +
188A LEU* 4.2 14.3 - - + +
200A LEU* 4.7 7.4 - - + -
204A ILE* 3.6 30.3 - - + -
214A ILE* 5.0 0.2 - - + -
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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