Contacts of the strand formed by residues 264 - 274 (chain D) in PDB entry 3TS8
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 264 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225B VAL* 3.5 37.3 - - + +
103D TYR* 4.2 17.5 - - + -
256D THR* 3.9 20.9 - - + -
257D LEU 3.9 2.7 - - - +
258D GLU* 4.7 1.8 - - + -
262D GLY 3.6 3.2 + - - -
263D ASN* 1.3 73.8 - - - +
265D LEU* 1.3 65.4 + - - +
266D GLY 3.3 28.9 - - - +
267D ARG* 3.2 44.2 - - + +
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Residues in contact with LEU 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D TYR* 3.9 6.1 - - - -
104D GLN 4.1 1.6 - - - +
105D GLY* 3.5 21.8 - - - -
106D SER* 4.2 4.8 + - - -
107D TYR* 4.2 31.1 - - + +
152D PRO* 4.4 7.9 - - + -
155D THR* 4.1 19.7 - - + +
257D LEU* 2.7 23.9 + - + +
258D GLU 3.9 4.7 - - - -
259D ASP* 3.8 32.1 - - + +
263D ASN* 3.9 10.5 - - + +
264D LEU* 1.3 81.3 - - - +
266D GLY* 1.3 59.6 + - - +
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Residues in contact with GLY 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D TYR* 3.2 15.9 - - - -
104D GLN 4.5 0.2 - - - -
109D PHE* 3.7 17.9 - - - -
256D THR* 3.3 2.3 - - - -
257D LEU* 2.7 32.1 + - - +
264D LEU* 3.3 9.4 - - - +
265D LEU* 1.3 81.5 - - - +
267D ARG* 1.3 62.2 + - - +
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Residues in contact with ARG 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224B GLU* 6.3 0.2 - - - -
225B VAL 3.0 24.0 + - - -
226B GLY* 3.2 22.2 + - - -
99D SER* 3.5 41.2 + - - +
100D GLN 4.6 1.3 - - - -
101D LYS 2.6 25.7 + - - +
102D THR* 3.6 4.4 - - - +
103D TYR* 2.7 39.6 + - + +
109D PHE* 3.5 7.9 - - - +
254D ILE* 3.9 11.0 - - + -
255D ILE 3.4 6.1 - - - -
256D THR* 3.7 22.9 - - + +
264D LEU* 3.2 33.2 - - + +
266D GLY* 1.3 76.0 - - - +
268D ASP* 1.3 68.6 + - - +
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Residues in contact with ASP 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D THR* 3.8 22.3 + - - +
109D PHE* 4.1 7.8 - - + +
110D ARG* 3.7 12.1 - - - +
111D LEU* 2.8 51.2 + - + +
254D ILE* 3.8 4.0 - - - +
255D ILE 3.0 28.7 + - - +
267D ARG* 1.3 78.4 - - - +
269D SER* 1.3 81.7 + - - +
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Residues in contact with SER 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D GLN 4.0 15.2 + - - -
102D THR* 4.9 4.5 + - - -
111D LEU* 4.0 3.1 - - - +
113D PHE* 5.4 0.3 - - - -
131D ASN* 3.1 16.7 + - - +
252D LEU* 4.5 11.0 - - - +
253D VAL 3.1 15.9 - - - -
254D ILE* 3.5 19.8 - - - +
268D ASP* 1.3 96.5 + - - +
270D PHE* 1.3 68.9 + - - +
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Residues in contact with PHE 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D LEU* 3.6 17.9 - - + -
113D PHE* 3.6 31.9 - + + -
126D TYR* 4.9 0.9 - + + -
131D ASN* 3.5 27.1 - - - +
133D MET* 4.3 15.3 - - + -
141D VAL* 5.5 1.6 - - + -
143D VAL* 4.2 21.8 - - + -
234D PHE* 5.2 3.6 - + - -
236D PHE* 5.0 7.9 - + - -
252D LEU* 3.7 6.3 - - - -
253D VAL* 3.0 51.5 + - + -
255D ILE* 4.1 8.7 - - + -
269D SER* 1.3 82.1 - - - +
271D GLU* 1.3 72.3 - - - +
272D VAL* 3.4 19.5 - - + -
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Residues in contact with GLU 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D LEU 4.9 4.7 - - - +
131D ASN* 2.9 13.1 + - - +
132D LYS* 2.9 47.9 + - + +
133D MET 2.9 22.2 + - - -
164D LYS* 2.6 44.6 + - + -
250D PRO* 4.2 9.3 - - - +
251D ILE 3.2 22.4 - - - +
252D LEU* 3.8 11.2 - - + +
270D PHE* 1.3 76.8 - - - +
272D VAL* 1.3 66.2 + - - +
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Residues in contact with VAL 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D LYS* 4.4 4.1 - - - -
133D MET* 3.6 13.5 - - + +
135D VAL* 4.7 4.3 - - + -
236D PHE* 4.2 22.9 - - + -
240D SER* 4.1 2.9 + - - -
250D PRO* 5.1 1.9 - - - +
251D ILE* 3.3 35.2 + - + +
253D VAL* 3.5 23.1 - - + -
270D PHE* 3.4 28.2 + - + -
271D GLU* 1.3 85.5 - - - +
273D ARG* 1.3 68.0 + - - +
274D VAL* 4.1 19.3 - - + -
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Residues in contact with ARG 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D LYS* 3.4 24.0 - - - +
133D MET 3.0 10.2 + - - +
134D PHE* 3.6 24.9 - - + -
135D VAL* 3.2 23.0 + - - +
240D SER* 3.5 15.8 - - - +
272D VAL* 1.3 73.6 - - - +
274D VAL* 1.3 65.1 + - - +
275D CYS* 3.4 22.4 + - - +
281D ASP* 2.9 33.6 + - - -
285D GLU* 3.6 16.6 + - - -
43L A 5.3 1.0 - - - +
44L T 2.8 49.9 + - - +
45L G 5.6 0.2 + - - -
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Residues in contact with VAL 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D VAL* 3.2 12.3 - - + +
136D GLN 3.7 2.2 - - - +
137D LEU* 3.5 36.1 - - - +
194D LEU* 5.6 0.4 - - + -
236D PHE* 3.5 31.2 - - + +
238D CYS 3.1 27.6 - - - +
239D ASN* 3.4 9.6 - - - +
240D SER* 2.9 38.6 + - - +
246D MET* 4.9 4.9 - - + -
251D ILE* 5.8 1.3 - - + -
272D VAL* 4.1 7.4 - - + -
273D ARG* 1.3 73.9 - - - +
275D CYS* 1.3 59.6 + - - +
45L G 4.4 1.6 + - - -
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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