Contacts of the strand formed by residues 109 - 115 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7L LYS* 3.0 30.2 + - + +
8L PHE 4.2 4.5 - - - +
12L VAL* 3.4 27.1 - - + -
103L GLY 3.9 5.6 - - - +
104L TRP* 3.8 37.7 - - + -
105L ASP* 4.8 0.3 - - - +
108L GLY* 1.3 88.6 - - - +
110L GLY* 1.3 58.5 + - - +
145L TYR* 3.3 26.0 - - - +
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Residues in contact with GLY 110 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7L LYS* 4.2 3.8 - - - -
12L VAL* 4.4 3.3 - - - +
76L VAL* 4.0 13.2 - - - -
102L CYS* 3.4 2.9 - - - +
103L GLY 2.9 36.1 + - - -
105L ASP* 4.0 13.2 - - - -
108L GLY 3.7 0.2 + - - -
109L PRO* 1.3 75.1 - - - +
111L LEU* 1.3 62.0 + - - +
112L TYR* 4.6 6.7 - - - -
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Residues in contact with LEU 111 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5L ALA* 3.5 39.5 - - + +
6L PHE* 3.5 13.0 - - - +
7L LYS* 4.2 18.0 - - + +
12L VAL* 4.3 4.9 - - + -
100L MET* 4.6 5.6 - - + -
101L ILE 3.5 12.8 - - - +
102L CYS* 4.0 12.1 - - + -
110L GLY* 1.3 73.6 - - - +
112L TYR* 1.3 78.5 + - - +
122L SER* 3.9 1.6 + - - -
123L GLY 3.2 24.1 + - - +
124L ALA 2.9 28.5 - - - +
126L PHE* 3.8 15.9 - - + -
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Residues in contact with TYR 112 (chain L).
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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99D GLU* 4.1 8.6 + - - -
7L LYS* 6.2 1.1 - - - -
76L VAL* 3.4 20.4 - - + -
77L ALA* 3.9 18.6 - - - +
80L SER* 3.3 31.2 - - - +
101L ILE 2.9 33.7 + - - +
105L ASP* 5.5 1.6 - - - -
110L GLY* 4.6 4.9 - - - -
111L LEU* 1.3 101.6 - - - +
113L TYR* 1.4 62.6 + - - +
114L VAL* 3.6 2.9 - - + +
120L ARG* 3.7 33.9 - - + -
121L ILE 3.4 8.1 - - - +
122L SER* 3.8 29.9 + - - -
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Residues in contact with TYR 113 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23K SER* 6.2 0.2 - - - -
28K MET* 3.8 31.9 - - + -
98L GLY* 4.0 7.0 - - - -
99L THR 3.9 5.2 - - - -
100L MET* 3.9 8.5 - - + -
112L TYR* 1.4 71.1 - - - +
114L VAL* 1.4 67.7 + - - +
115L ASP* 2.9 46.1 + - + +
119L ASN* 3.4 1.9 - - + +
120L ARG* 3.4 0.2 - - - -
121L ILE* 2.9 47.0 + - + +
126L PHE* 3.4 48.6 - + + -
128L VAL* 3.6 42.2 - - + +
136L TYR* 5.7 0.4 - - - -
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Residues in contact with VAL 114 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80L SER* 3.7 28.0 - - - +
83L LEU* 4.0 22.9 - - + -
84L ALA* 4.2 22.2 - - + -
87L VAL* 5.0 2.5 - - + -
99L THR* 2.8 45.3 + - + +
101L ILE* 4.4 7.6 - - + -
112L TYR 3.6 12.3 - - - +
113L TYR* 1.4 83.0 - - - +
115L ASP* 1.3 68.5 + - - +
119L ASN 3.6 3.6 - - - -
120L ARG* 4.2 7.2 - - + +
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Residues in contact with ASP 115 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23K SER* 5.7 6.0 + - - -
28K MET* 6.0 1.1 - - + -
87L VAL* 3.8 7.6 - - - +
96L SER* 5.4 0.5 + - - -
97L MET* 3.2 16.4 - - - +
99L THR* 5.8 0.2 - - - -
113L TYR* 2.9 30.9 + - + +
114L VAL* 1.3 76.4 - - - +
116L SER* 1.3 66.2 + - - +
117L GLU* 3.2 30.9 + - - +
118L GLY* 3.2 17.7 + - - -
119L ASN* 3.2 38.1 + - + -
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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