Contacts of the strand formed by residues 104 - 108 (chain A) in PDB entry 5YUY
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 GLU 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A HIS* 2.7 27.6 + - - +
7A VAL 3.1 14.4 - - - +
8A ASP* 3.7 4.0 - - - +
86A ILE* 4.7 1.7 - - - +
87A ARG* 5.3 0.9 + - - -
90A PHE* 5.0 2.7 - - - -
99A PRO* 3.5 2.4 - - - +
100A LEU* 3.1 37.8 + - + +
101A SER* 3.3 25.3 + - - +
102A LEU 3.5 2.6 + - - -
103A ASP* 1.3 79.4 - - - +
105A ALA* 1.3 64.9 + - - +
150A LYS* 2.9 26.0 + - - -
902A MG 2.1 28.7 - - - -
901C TTP 5.2 0.5 + - - -
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Residues in contact with ALA 105 (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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5A ILE 3.8 0.3 - - - +
6A HIS* 3.4 9.1 - - - -
7A VAL* 3.0 30.8 + - - +
87A ARG* 5.9 0.4 - - + -
90A PHE* 3.6 30.4 - - + -
97A ILE* 4.0 12.1 - - + -
98A GLU 3.4 12.8 - - - +
99A PRO* 3.8 9.0 - - + -
100A LEU* 4.2 2.5 - - - +
104A GLU* 1.3 78.4 - - - +
106A TYR* 1.3 61.2 + - - +
107A LEU* 4.1 2.8 + - + +
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Residues in contact with TYR 106 (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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4A ILE* 3.9 11.2 - - + -
5A ILE 3.2 5.6 - - - +
6A HIS* 3.7 29.8 - + + -
96A ARG 3.8 0.5 - - - +
97A ILE* 3.4 0.3 - - - -
98A GLU* 2.8 39.8 + - + +
100A LEU* 3.5 36.7 - - + +
105A ALA* 1.3 72.6 - - - +
107A LEU* 1.3 65.6 + - - +
108A ASP 4.4 0.2 - - - -
146A LYS* 3.3 68.4 + - + +
147A PHE* 4.2 2.6 + - - -
149A ALA* 4.6 0.2 - - + -
150A LYS* 3.4 19.0 - - + +
182A PRO* 5.3 1.6 - - - +
232A ARG* 4.5 7.1 + - - -
234A VAL* 4.0 16.9 - - + +
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Residues in contact with LEU 107 (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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4A ILE* 3.4 6.4 - - - +
5A ILE* 2.8 46.1 + - + +
7A VAL* 4.8 7.6 - - + -
90A PHE* 3.9 29.4 - - + +
93A TYR* 4.9 1.1 - - + -
94A THR* 4.1 19.7 - - + -
96A ARG 3.3 5.2 - - - +
97A ILE* 3.7 28.0 - - + -
105A ALA* 4.2 4.5 - - + +
106A TYR* 1.3 86.0 - - - +
108A ASP* 1.3 60.5 + - - +
109A VAL* 3.8 9.8 + - + -
126A ILE* 3.6 31.2 - - + -
234A VAL* 4.4 3.1 - - - -
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Residues in contact with ASP 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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2A ARG* 3.7 17.0 - - - +
3A LYS 3.7 3.1 - - - +
4A ILE* 3.7 16.0 - - + +
94A THR* 3.4 20.0 + - - -
96A ARG* 3.1 51.0 + - + +
107A LEU* 1.3 70.4 - - - +
109A VAL* 1.3 59.6 + - - +
110A THR* 2.7 32.6 + - - -
111A ASP 4.7 1.0 + - - -
233A ASP* 4.3 1.0 - - - +
234A VAL* 3.8 22.0 - - + +
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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