Contacts of the strand formed by residues 109 - 115 (chain Z) in PDB entry 5A0Q
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 PRO 109 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7Z LYS* 3.0 30.8 + - + +
8Z PHE 4.2 4.9 - - - +
12Z VAL* 3.4 26.2 - - + -
103Z GLY 3.9 5.8 - - - +
104Z TRP* 3.8 37.4 - - + -
105Z ASP* 4.8 0.3 - - - +
108Z GLY* 1.3 88.0 - - - +
110Z GLY* 1.3 58.3 + - - +
145Z TYR* 3.3 26.0 - - - +
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Residues in contact with GLY 110 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7Z LYS* 4.2 3.4 - - - -
12Z VAL* 4.4 3.3 - - - +
76Z VAL* 4.0 14.1 - - - -
102Z CYS* 3.4 2.4 - - - +
103Z GLY 2.9 36.6 + - - -
105Z ASP* 4.0 13.2 - - - -
109Z PRO* 1.3 75.0 - - - +
111Z LEU* 1.3 60.8 + - - +
112Z TYR* 4.6 6.7 - - - -
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Residues in contact with LEU 111 (chain Z).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5Z ALA* 3.5 39.0 - - + +
6Z PHE* 3.5 13.2 - - - +
7Z LYS* 4.2 18.4 + - + +
12Z VAL* 4.3 4.5 - - + -
100Z MET* 4.6 5.4 - - + -
101Z ILE 3.5 11.9 - - - +
102Z CYS* 4.0 13.0 - - + -
110Z GLY* 1.3 73.6 - - - +
112Z TYR* 1.3 80.3 + - - +
122Z SER* 3.9 1.4 + - - -
123Z GLY 3.2 25.0 + - - +
124Z ALA 2.9 27.8 - - - +
126Z PHE* 3.8 15.9 - - + -
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Residues in contact with TYR 112 (chain Z).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99R GLU* 4.1 8.3 + - - -
7Z LYS* 6.2 0.7 - - - -
76Z VAL* 3.4 21.3 - - + -
77Z ALA* 3.9 17.6 - - - +
80Z SER* 3.3 30.7 - - - +
100Z MET* 3.7 0.2 - - - -
101Z ILE 2.9 33.5 + - - +
105Z ASP* 5.5 1.8 - - - -
110Z GLY* 4.6 4.9 - - - -
111Z LEU* 1.3 101.4 - - - +
113Z TYR* 1.4 62.6 + - - +
114Z VAL* 3.6 2.8 - - + +
120Z ARG* 3.7 33.9 - - + -
121Z ILE 3.4 7.6 - - - +
122Z SER* 3.8 29.9 + - - -
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Residues in contact with TYR 113 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28Y MET* 3.8 31.2 - - + -
98Z GLY* 4.0 7.1 - - - -
99Z THR 3.9 5.2 - - - -
100Z MET* 3.9 7.9 - - + -
112Z TYR* 1.4 70.3 - - - +
114Z VAL* 1.4 68.8 + - - +
115Z ASP* 2.9 45.4 + - + +
119Z ASN* 3.4 2.6 - - + +
120Z ARG 3.6 0.2 - - - -
121Z ILE* 2.9 46.7 + - + +
126Z PHE* 3.4 49.5 - + + -
128Z VAL* 3.6 42.7 - - + +
136Z TYR* 6.0 0.4 - - - -
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Residues in contact with VAL 114 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80Z SER* 3.7 28.3 - - - +
83Z LEU* 4.0 23.1 - - + -
84Z ALA* 4.2 21.5 - - + -
87Z VAL* 5.0 2.2 - - + -
98Z GLY* 4.0 0.3 - - - -
99Z THR* 2.8 46.7 + - + +
101Z ILE* 4.4 8.3 - - + -
112Z TYR 3.6 11.9 - - - +
113Z TYR* 1.4 83.3 - - - +
115Z ASP* 1.3 67.1 + - - +
119Z ASN 3.6 3.4 - - - -
120Z ARG* 4.4 7.0 - - + -
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Residues in contact with ASP 115 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23Y SER* 5.7 5.3 + - - -
28Y MET* 6.0 1.1 - - + -
87Z VAL* 3.8 7.7 - - - +
96Z SER* 5.4 0.7 + - - -
97Z MET* 3.2 16.3 - - - +
98Z GLY* 4.6 0.2 - - - -
113Z TYR* 2.9 31.7 + - + +
114Z VAL* 1.3 77.5 - - - +
116Z SER* 1.3 66.3 + - - +
117Z GLU* 3.2 30.9 + - - +
118Z GLY* 3.2 17.3 + - - -
119Z ASN* 3.2 39.4 + - + -
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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