Contacts of the strand formed by residues 269 - 274 (chain D) in PDB entry 1TLF
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 SER 269 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174D LEU* 4.6 6.5 - - - -
179D HIS* 3.7 7.6 + - - -
240D THR 2.8 15.8 + - - -
241D ALA* 3.0 11.2 - - - -
242D MET 2.5 30.5 + - - -
265D GLY 3.1 20.3 + - - +
267D ASP 4.0 0.6 + - - -
268D ILE* 1.3 76.3 - - - +
270D VAL* 1.3 58.6 + - - +
328D THR 3.3 10.2 + - - -
329D THR* 4.2 2.9 - - - -
330D LEU 3.1 26.3 + - - -
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Residues in contact with VAL 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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242D MET* 3.4 10.5 - - + +
244D VAL* 4.0 22.2 - - + -
250D ALA* 4.1 26.2 - - + +
253D ALA* 4.7 2.2 - - + -
254D MET* 4.5 4.3 - - + +
257D ILE* 3.4 33.4 - - + -
264D VAL* 3.9 11.7 - - + -
268D ILE 4.0 0.2 - - - +
269D SER* 1.3 81.6 - - - +
271D VAL* 1.3 69.0 + - - +
286D LEU* 4.2 6.1 - - + -
287D THR* 4.1 2.1 - - - +
328D THR* 3.0 40.6 + - - +
329D THR* 4.8 0.7 - - - -
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Residues in contact with VAL 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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170D GLY* 4.5 13.0 - - - +
173D HIS* 4.4 8.5 - - + +
174D LEU* 4.0 28.7 - - + -
242D MET 2.7 14.5 + - - +
243D LEU* 3.7 22.0 - - + -
244D VAL* 2.7 34.3 + - - +
270D VAL* 1.3 80.5 - - - +
272D GLY* 1.3 70.3 + - - +
287D THR* 3.9 20.2 - - + +
288D THR* 4.7 3.4 - - - -
289D ILE* 4.5 8.1 - - + -
323D LEU* 4.8 4.0 - - + -
329D THR* 5.3 1.1 - - - -
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Residues in contact with GLY 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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244D VAL* 3.6 7.4 - - - +
246D ASN 4.4 0.7 - - - -
247D ASP* 3.6 6.5 - - - -
250D ALA* 4.0 18.2 - - - -
271D VAL* 1.3 88.0 - - - +
273D TYR* 1.3 64.0 + - - +
286D LEU* 4.1 2.8 - - - +
287D THR 3.1 15.2 + - - -
288D THR* 3.1 13.1 + - - -
289D ILE* 3.5 8.8 + - - +
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Residues in contact with TYR 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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162D SER 4.1 0.5 + - - -
163D HIS* 3.8 18.7 + - - -
166D GLY* 3.2 35.2 - - - -
167D THR* 3.8 8.5 + - + -
197D ARG* 3.7 40.2 + - + +
201D TRP* 4.4 12.6 - + - -
244D VAL 3.6 5.6 - - - +
245D ALA 3.2 23.6 - - - +
246D ASN* 3.1 1.4 - - - -
247D ASP* 2.9 29.1 + - - +
272D GLY* 1.3 77.0 - - - -
274D ASP* 1.3 75.7 + - - +
288D THR* 3.4 2.2 - - - -
289D ILE* 3.8 22.9 - - + +
291D GLN* 3.0 31.7 + - - -
321D VAL* 4.7 0.2 - - - +
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Residues in contact with ASP 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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75D ALA* 4.0 3.8 - - - +
197D ARG* 4.1 0.3 + - - -
246D ASN* 3.7 2.3 + - - +
247D ASP* 4.3 3.0 + - - +
273D TYR* 1.3 81.3 - - - +
275D ASP* 1.3 65.0 + - - +
276D THR* 3.3 19.6 + - + +
289D ILE 2.7 15.5 + - - -
290D LYS* 4.2 0.3 - - - +
291D GLN* 2.8 48.4 + - - +
293D PHE* 3.2 18.7 - - + -
998D IPT 2.6 48.4 + - - -
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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