Contacts of the strand formed by residues 110 - 115 (chain A) in PDB entry 3A4T
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 THR 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A ASP 2.9 9.9 + - - +
86A PHE* 4.0 11.7 - - + -
87A ILE* 2.8 29.1 + - - +
105A MET* 3.9 0.8 - - - +
108A LYS 3.6 1.0 + - - -
109A GLY* 1.3 82.4 + - - -
111A ILE* 1.3 73.3 + - - +
112A VAL* 4.3 0.4 - - + -
135A ASN* 3.1 7.6 - - - +
137A ILE* 3.7 30.5 - - + -
28B ARG* 4.3 5.2 + - - -
58B PRO* 3.3 33.6 - - + +
62B PHE* 3.7 14.4 - - + -
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Residues in contact with ILE 111 (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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87A ILE* 3.2 16.4 - - + +
89A ASP* 4.1 14.1 - - + +
98A THR* 3.5 43.1 - - + +
101A LEU* 3.8 9.6 - - + -
102A ALA* 3.6 18.2 - - + +
105A MET* 3.9 15.3 - - - -
110A THR* 1.3 81.6 - - - +
112A VAL* 1.3 75.4 + - - +
113A ALA 4.2 0.4 - - - +
135A ASN* 2.7 17.9 + - - +
136A THR* 3.2 19.4 - - + +
137A ILE* 2.8 27.4 + - - -
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Residues in contact with VAL 112 (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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86A PHE* 3.7 29.2 - - + -
87A ILE 2.7 9.2 + - - +
88A LEU* 3.3 25.1 - - + +
89A ASP 2.8 30.8 + - - -
110A THR* 4.3 5.4 - - + -
111A ILE* 1.3 74.5 - - - +
113A ALA* 1.3 56.5 + - - +
114A VAL* 4.0 4.9 - - + -
137A ILE* 3.6 11.0 - - + +
139A ILE* 3.8 26.5 - - + -
146A TYR* 4.2 13.5 - - + +
150A LEU* 5.5 0.2 - - + -
157A PHE* 3.8 7.4 - - + -
61B LEU* 4.1 15.5 - - + -
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Residues in contact with ALA 113 (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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89A ASP* 3.7 6.1 - - + -
92A ALA* 3.8 17.3 - - + -
98A THR* 3.9 13.0 - - + -
111A ILE* 3.7 1.2 - - + -
112A VAL* 1.3 71.8 - - - +
114A VAL* 1.3 57.3 + - - +
124A LEU* 4.2 12.6 - - + -
136A THR* 3.6 24.9 - - + -
137A ILE 3.0 7.6 + - - +
138A ILE* 3.5 5.4 - - - +
139A ILE 2.8 32.1 + - - +
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Residues in contact with VAL 114 (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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88A LEU* 3.9 18.8 - - + -
89A ASP 3.0 6.6 + - - +
90A MET 3.1 19.1 - - - +
91A CYS* 3.4 0.5 - - - -
92A ALA* 2.7 32.5 + - - +
112A VAL* 4.0 6.5 - - + -
113A ALA* 1.3 76.9 - - - +
115A GLU* 1.3 60.3 + - - +
139A ILE* 3.4 26.9 - - + +
141A ALA 3.4 21.8 - - - +
143A MET* 3.7 36.3 - - + +
146A TYR* 4.1 8.5 - - + -
500A SFG 4.3 0.4 - - + -
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Residues in contact with GLU 115 (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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92A ALA 3.6 2.1 + - - -
93A ALA* 3.1 34.0 + - + +
114A VAL* 1.3 76.3 - - - +
116A ILE* 1.3 60.0 + - - +
117A SER* 3.3 33.0 + - - +
120A ARG* 3.7 2.0 - - + +
121A THR* 3.6 14.1 - - + +
124A LEU* 4.6 11.2 - - + -
139A ILE 3.1 8.6 + - - +
140A ASN* 3.0 13.9 - - - +
141A ALA 3.0 19.4 + - - -
500A SFG 2.3 55.4 + - - -
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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