Contacts of the strand formed by residues 110 - 115 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B ASP 3.1 8.5 + - - +
86B PHE* 3.6 31.8 - - + -
87B ILE* 2.9 28.2 + - - +
105B MET* 3.9 1.6 - - - +
108B LYS 3.7 1.0 + - - -
109B GLY* 1.3 76.0 + - - -
111B ILE* 1.3 75.4 + - - +
112B VAL* 4.4 0.9 - - + -
135B ASN 3.3 8.5 + - - +
137B ILE* 3.9 28.7 - - + +
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Residues in contact with ILE 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ILE* 3.6 15.7 - - + +
89B ASP* 4.0 11.0 - - + +
98B THR* 3.7 32.3 - - + +
101B LEU* 3.8 10.3 - - + -
102B ALA* 3.6 24.2 - - - +
105B MET* 3.9 11.0 - - - -
110B THR* 1.3 80.0 - - - +
112B VAL* 1.3 70.0 + - - +
113B ALA 4.1 0.2 - - - +
135B ASN* 2.8 37.9 + - - +
136B THR* 3.2 11.0 - - - +
137B ILE* 2.6 35.2 + - - +
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Residues in contact with VAL 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B PHE* 4.1 17.7 - - + -
87B ILE 3.1 9.8 + - - +
88B LEU* 3.3 15.1 - - + +
89B ASP 2.8 29.1 + - - -
110B THR* 4.4 5.6 - - + -
111B ILE* 1.3 75.2 - - - +
113B ALA* 1.3 54.5 + - - +
114B VAL* 4.1 13.9 - - + -
137B ILE* 3.4 14.8 - - + +
139B ILE* 3.7 29.4 - - + -
146B TYR* 4.1 9.4 - - + +
150B LEU* 5.9 0.7 - - + -
157B PHE* 3.9 23.3 - - + -
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Residues in contact with ALA 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B ASP* 3.6 8.5 - - - -
92B ALA* 3.5 18.8 - - + -
98B THR* 3.7 25.4 - - + -
111B ILE 3.6 0.8 - - - -
112B VAL* 1.3 71.5 - - - +
114B VAL* 1.3 61.8 + - - +
124B LEU* 4.3 11.3 - - + +
136B THR* 3.9 13.9 - - + -
137B ILE 2.9 6.5 + - - +
138B ILE* 3.5 4.6 - - + +
139B ILE* 3.0 24.9 + - - +
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Residues in contact with VAL 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B LEU* 3.9 23.3 - - + -
89B ASP 2.9 9.4 + - - +
90B MET 3.3 17.2 - - - +
91B CYS* 3.5 0.5 - - - -
92B ALA* 2.8 27.3 + - - -
112B VAL* 4.1 6.3 - - + -
113B ALA* 1.3 76.6 - - - +
115B GLU* 1.3 64.3 + - - +
139B ILE* 3.3 15.0 - - + +
141B ALA* 3.3 26.5 - - + +
143B MET* 4.0 15.0 - - - +
146B TYR* 3.9 24.0 - - + -
501B SFG 4.1 8.7 - - + -
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Residues in contact with GLU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B ALA 4.0 1.0 + - - -
93B ALA* 3.2 24.0 + - + -
113B ALA 4.2 0.2 + - - -
114B VAL* 1.3 74.8 - - - +
116B ILE* 1.3 62.0 + - - +
117B SER* 2.9 38.7 + - - +
120B ARG* 3.9 2.3 - - - +
121B THR* 3.4 13.9 - - - +
124B LEU* 4.2 16.4 - - + +
139B ILE 2.9 7.7 + - - -
140B ASN* 3.2 7.3 - - - +
141B ALA 3.0 23.4 + - - -
501B SFG 2.3 56.6 + - - -
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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