Contacts of the strand formed by residues 144 - 149 (chain B) in PDB entry 3T0E
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 LEU 144 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B VAL* 5.0 2.7 - - + -
131B TYR 3.9 3.6 - - - -
132B PRO* 4.3 6.7 - - + -
143B LEU* 1.3 84.5 - - - +
145B VAL* 1.3 65.3 + - - +
160B TRP* 3.2 45.1 - - + -
189B MET* 3.8 1.4 - - - +
190B LEU* 3.1 34.9 + - + +
192B THR* 4.5 5.6 - - - +
200B TYR* 3.3 30.7 - - + -
217B TRP* 3.9 42.6 - - + +
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Residues in contact with VAL 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B VAL* 3.0 24.5 - - - +
131B TYR* 2.7 68.7 + - + +
133B ALA* 4.2 2.0 - - + -
143B LEU* 3.9 18.2 - - + -
144B LEU* 1.3 79.9 - - - +
146B CYS* 1.3 69.8 + - - +
147B SER 4.2 0.2 - - - -
160B TRP* 4.1 1.8 - - - -
187B LEU* 4.3 17.0 - - + -
188B VAL 4.0 3.8 - - - -
189B MET* 4.1 13.7 - - + +
40E TYR* 4.0 11.4 - - + +
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Residues in contact with CYS 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B VAL* 4.1 11.2 - - - -
129B THR 4.1 11.0 - - - +
130B VAL* 5.0 0.2 - - + -
145B VAL* 1.3 80.8 - - - +
147B SER* 1.3 59.8 + - - +
148B VAL* 3.8 7.1 + - - +
158B VAL* 4.3 8.7 - - - -
160B TRP* 3.7 9.6 - - + +
186B THR 3.5 5.2 - - - +
187B LEU* 3.7 0.7 - - - -
188B VAL* 3.1 40.2 + - + +
202B CYS* 2.0 45.5 - - + -
204B VAL* 5.1 0.2 - - - -
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Residues in contact with SER 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A PRO* 3.7 28.2 - - - +
128B VAL* 3.4 1.8 - - - -
129B THR* 3.0 33.6 + - - -
130B VAL* 4.7 0.4 - - - +
131B TYR* 4.1 15.3 + - - -
145B VAL 4.2 0.6 - - - -
146B CYS* 1.3 72.1 - - - +
148B VAL* 1.3 61.0 + - - +
149B ASN* 3.2 19.9 + - - -
185B GLN* 4.9 0.9 + - - -
186B THR 3.8 2.7 - - - -
187B LEU* 3.2 25.2 - - - +
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Residues in contact with VAL 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B PRO* 4.0 14.1 - - + +
127B GLU 3.7 4.0 - - - +
128B VAL* 4.5 6.5 - - + +
146B CYS* 4.5 8.1 - - - +
147B SER* 1.3 71.9 + - - +
149B ASN* 1.3 74.3 + - - +
151B PHE* 3.5 34.8 - - + -
156B ILE* 3.9 7.4 - - + -
158B VAL* 3.9 26.7 - - + -
185B GLN* 3.5 2.6 - - - +
186B THR* 3.2 37.8 + - + +
188B VAL* 5.9 0.7 - - + -
204B VAL* 3.9 15.0 - - + -
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Residues in contact with ASN 149 (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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94A ASN* 3.1 26.5 - - - +
95A SER* 3.6 17.4 - - - -
96A PRO* 3.6 13.1 - - - +
126B PRO* 3.6 2.6 - - - +
127B GLU* 2.8 46.4 + - + +
129B THR* 4.3 2.4 + - - -
147B SER* 3.2 27.8 + - - -
148B VAL* 1.3 84.1 + - - +
150B GLY* 1.3 66.9 + - - +
151B PHE* 3.5 5.0 + - - -
184B PHE 4.2 4.3 - - - +
185B GLN* 3.7 12.8 + - - +
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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