Contacts of the strand formed by residues 284 - 292 (chain A) in PDB entry 1TFZ
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 GLY 284 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A TYR* 4.0 7.7 - - - -
164A VAL* 3.7 17.3 - - - -
208A GLY* 3.4 1.2 - - - -
209A ASN 2.9 27.1 + - - +
276A TYR* 3.1 18.4 + - - -
280A ASN* 4.0 4.3 - - - -
282A GLY 3.9 0.6 + - - -
283A ALA* 1.3 76.9 - - - +
285A LEU* 1.3 60.0 + - - -
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Residues in contact with LEU 285 (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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118A VAL* 3.4 43.4 + - + +
121A VAL* 4.0 19.3 - - + -
161A TYR* 2.9 31.6 - - + +
164A VAL* 3.9 9.4 - - + +
206A ALA* 4.2 8.3 - - + -
207A VAL 3.5 14.4 - - - +
208A GLY* 4.1 0.2 - - - -
276A TYR* 2.7 17.9 + - - -
284A GLY* 1.3 69.7 - - - -
286A GLN* 1.3 61.1 + - - +
287A HIS 4.5 4.3 - - - +
288A LEU* 3.3 35.2 - - + -
370A ILE* 3.8 14.1 - - + +
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Residues in contact with GLN 286 (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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207A VAL* 2.6 16.4 + - - +
209A ASN* 3.5 35.2 - - - +
244A LEU* 5.6 1.4 - - - +
261A ASN* 3.3 13.3 + - - +
272A GLN* 6.3 0.4 - - - +
273A ILE* 3.8 22.4 - - - +
276A TYR* 3.9 11.2 - - + -
284A GLY 3.4 2.2 + - - -
285A LEU* 1.3 73.4 - - - +
287A HIS* 1.3 88.2 + - - +
370A ILE* 3.1 9.0 - - - -
371A PHE* 3.1 46.6 + - + -
551A 869 4.9 9.1 - - - +
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Residues in contact with HIS 287 (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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205A HIS* 4.0 2.6 - - - +
206A ALA* 3.6 1.9 - - - -
207A VAL* 3.0 46.1 + - + +
285A LEU* 3.7 1.8 - - - +
286A GLN* 1.3 109.6 + - - +
288A LEU* 1.3 67.7 + - - +
289A ALA 4.4 0.2 - - - -
370A ILE* 4.6 2.0 - - - -
371A PHE* 3.1 37.1 - + + +
372A ILE* 4.9 0.7 - - - -
373A GLU* 3.4 18.6 - - + -
425A FE 2.4 28.3 - - - -
551A 869 3.1 33.4 + + + -
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Residues in contact with LEU 288 (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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29A ILE* 4.0 23.8 - - + -
31A PHE* 3.8 22.0 - - + -
76A PHE* 3.8 24.9 - - + -
118A VAL* 4.1 4.7 - - + -
203A LEU* 4.1 11.7 - - + -
205A HIS 3.7 2.2 - - - -
206A ALA* 4.0 15.3 - - + -
285A LEU* 3.3 30.5 - - + -
287A HIS* 1.3 76.6 - - - +
289A ALA* 1.3 59.8 + - - +
290A LEU* 3.7 6.5 + - + +
370A ILE* 4.4 7.2 - - + -
371A PHE 3.4 4.4 + - - -
372A ILE* 3.6 16.0 - - + +
373A GLU 2.9 23.4 + - - +
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Residues in contact with ALA 289 (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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203A LEU* 3.5 5.7 - - - +
204A ASP* 2.8 31.5 + - + -
205A HIS* 2.9 53.1 + - + +
287A HIS* 4.1 1.6 - - - -
288A LEU* 1.3 70.0 - - - +
290A LEU* 1.3 61.7 + - - +
373A GLU* 3.3 24.0 - - + +
375A ILE* 4.5 3.6 - - + -
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Residues in contact with LEU 290 (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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47A LEU* 4.1 6.5 - - + -
49A MET* 5.7 0.2 - - - -
74A LEU* 3.8 22.7 - - + -
76A PHE* 3.8 24.2 - - + -
200A ILE* 3.8 31.0 - - + -
202A ARG 3.6 2.7 - - - +
203A LEU* 3.8 17.5 - - + -
288A LEU* 4.1 6.5 - - + +
289A ALA* 1.3 77.1 - - - +
291A MET* 1.3 63.8 + - - +
292A SER 3.5 0.5 + - - -
372A ILE* 3.8 33.2 - - + -
373A GLU 2.7 16.2 + - - +
374A ILE* 3.5 10.7 - - + +
375A ILE* 3.0 23.2 + - - +
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Residues in contact with MET 291 (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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200A ILE* 3.5 4.2 - - - +
201A ARG* 2.7 53.9 + - + -
202A ARG* 2.7 60.4 + - + +
204A ASP* 4.4 9.6 - - + +
289A ALA 3.9 2.0 + - - -
290A LEU* 1.3 71.9 - - - +
292A SER* 1.3 71.1 + - - +
293A GLU* 3.9 4.7 - - + -
375A ILE* 3.3 17.8 - - + +
376A GLN* 5.2 4.3 - - + -
377A ARG* 5.8 2.5 - - + +
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Residues in contact with SER 292 (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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199A GLY 3.5 8.1 + - - -
200A ILE* 4.2 2.2 - - - +
291A MET* 1.3 80.4 - - - +
293A GLU* 1.3 56.9 + - - +
294A ASP 3.1 17.2 + - - -
295A ILE* 4.0 13.0 - - - -
298A THR* 2.7 27.8 + - - -
374A ILE* 4.0 15.5 - - - -
375A ILE 2.8 13.3 + - - -
376A GLN* 3.1 27.5 - - - +
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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