Contacts of the strand formed by residues 215 - 220 (chain A) in PDB entry 3TR6
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 215 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A GLN* 3.8 31.2 - - + +
52A LEU* 3.5 29.2 - - + -
53A LEU* 4.2 14.1 - - + -
56A LEU* 5.2 0.2 - - + -
142A TYR* 4.1 10.8 - - + -
168A ALA* 4.0 8.5 - - + -
169A VAL 3.4 30.5 - - - +
172A VAL* 4.0 0.8 - - - +
208A LEU* 4.3 0.9 - - - +
209A ILE* 2.8 44.6 + - + +
211A ILE* 3.8 6.5 + - + +
214A GLY* 1.3 72.8 - - - -
216A THR* 1.3 59.8 + - - +
217A LEU* 3.7 21.2 + - + -
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Residues in contact with THR 216 (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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154A TYR* 6.4 0.4 - - + -
167A ILE 3.4 1.4 - - - +
168A ALA* 3.3 5.5 - - - -
169A VAL* 2.9 41.8 + - + +
172A VAL* 3.5 32.2 - - - +
194A PHE* 5.6 1.7 - - + -
195A ASN* 4.7 2.3 + - - -
198A VAL* 4.1 18.4 - - + -
206A MSE 3.9 20.2 - - + +
207A ILE 3.3 10.1 - - - +
208A LEU* 3.6 12.8 - - - +
215A LEU* 1.3 72.2 - - - +
217A LEU* 1.3 70.4 + - - +
218A ALA* 4.8 2.7 - - + +
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Residues in contact with LEU 217 (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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52A LEU* 5.2 4.9 - - + -
56A LEU* 4.1 29.2 - - + -
166A LEU* 4.0 16.8 - - + -
167A ILE 3.3 2.7 - - - +
168A ALA* 3.8 22.9 - - + -
206A MSE 2.9 28.0 - - - +
207A ILE* 2.8 36.5 + - + +
209A ILE* 4.2 13.0 - - + -
215A LEU* 3.8 22.7 - - + +
216A THR* 1.3 80.9 - - - +
218A ALA* 1.3 59.9 + - - +
219A ARG 4.2 0.4 - - - -
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Residues in contact with ALA 218 (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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154A TYR* 4.3 20.0 - - + +
161A LEU* 4.7 0.5 - - - +
165A GLY 3.8 0.2 - - - +
166A LEU* 3.6 4.4 - - - +
167A ILE* 2.9 45.0 + - + +
169A VAL* 6.5 0.2 - - + -
198A VAL* 4.8 4.9 - - + -
204A VAL* 4.0 27.4 - - + +
205A ASP 3.3 4.3 - - - -
206A MSE 4.2 4.5 - - + -
216A THR* 4.2 2.7 - - + -
217A LEU* 1.3 74.1 - - - +
219A ARG* 1.3 63.1 + - - +
220A LYS 3.7 1.4 + - - -
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Residues in contact with ARG 219 (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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163A GLU* 5.2 1.2 - - - +
164A GLY* 3.6 30.2 + - - +
165A GLY 3.3 12.3 - - - +
166A LEU* 3.8 11.3 - - + +
204A VAL* 3.1 6.4 - - - -
205A ASP* 2.7 56.1 + - + +
218A ALA* 1.3 72.0 - - - +
220A LYS* 1.3 71.4 + - - +
221A LYS* 3.2 13.2 + - - +
222A SER* 4.7 12.3 + - - +
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Residues in contact with LYS 220 (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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136A TRP* 3.5 40.3 - - + -
158A LEU* 2.9 48.9 + - + +
159A LYS* 4.1 4.6 + - - +
161A LEU* 2.9 30.5 + - + +
162A ARG 3.5 16.2 - - - +
164A GLY* 2.8 32.0 + - - +
165A GLY 2.9 13.6 + - - +
203A ARG* 3.8 7.9 - - + +
204A VAL* 4.3 4.4 - - - +
218A ALA 3.7 2.6 + - - -
219A ARG* 1.3 71.8 + - - +
221A LYS* 1.3 68.7 + - - +
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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