Contacts of the strand formed by residues 315 - 322 (chain B) in PDB entry 1TTT
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 LYS 315 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B HIS* 4.9 0.2 - - - +
314B THR* 1.3 79.4 - - - +
316B PHE* 1.3 61.6 + - - +
354B ARG* 5.2 0.4 - - - +
371B THR* 4.4 9.2 - - - +
372B VAL 3.0 3.4 - - - +
373B GLU* 3.6 41.2 + - + +
380B LEU* 5.2 0.2 - - - +
403B ILE* 3.6 4.0 - - - +
404B LEU* 2.6 54.7 + - + +
405B GLU* 2.6 53.8 + - + +
24D G 5.5 9.7 + - - -
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Residues in contact with PHE 316 (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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315B LYS* 1.3 83.1 - - - +
317B GLU* 1.3 68.5 + - - +
318B ALA* 3.5 19.7 - - + -
342B PHE* 4.5 6.1 - + - -
344B PHE* 3.9 18.6 - + - -
371B THR* 3.1 3.8 - - - -
372B VAL* 2.6 68.4 + - + -
374B LEU* 3.7 26.2 - - + -
380B LEU* 3.6 22.7 - - + -
386B PHE* 4.0 10.8 - + - -
400B VAL* 3.8 17.9 - - + -
402B LYS 2.9 18.2 - - - +
403B ILE* 4.1 2.5 - - - -
404B LEU* 3.0 13.6 - - - +
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Residues in contact with GLU 317 (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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316B PHE* 1.3 76.2 - - - +
318B ALA* 1.3 65.2 + - - +
369B THR* 4.9 10.5 - - + -
370B PHE 3.3 11.9 - - - +
371B THR* 4.5 6.9 + - - +
401B THR* 2.7 32.4 + - + +
402B LYS* 2.9 43.2 + - + +
404B LEU* 3.2 19.0 - - + +
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Residues in contact with ALA 318 (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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316B PHE* 3.5 25.4 - - + +
317B GLU* 1.3 80.1 - - - +
319B SER* 1.3 60.8 + - - +
320B VAL* 3.8 6.9 + - + +
369B THR* 3.4 5.8 - - - +
370B PHE 3.0 30.4 + - - +
372B VAL* 5.2 3.6 - - + -
386B PHE* 3.6 19.7 - - + -
399B VAL 3.4 9.9 - - - +
401B THR* 3.6 5.8 - - - +
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Residues in contact with SER 319 (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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318B ALA* 1.3 70.3 - - - +
320B VAL* 1.3 66.4 + - - +
368B VAL 4.4 1.7 + - - -
369B THR* 4.0 14.4 - - - -
398B GLY* 3.2 2.6 - - - -
399B VAL* 3.2 39.6 + - - +
401B THR* 3.5 13.1 + - - -
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Residues in contact with VAL 320 (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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318B ALA* 3.8 20.6 + - + +
319B SER* 1.3 86.2 + - - +
321B TYR* 1.3 81.7 + - - +
322B ILE* 4.1 11.2 - - + -
367B ASN* 3.2 8.4 - - - +
368B VAL* 3.2 31.3 + - + +
370B PHE* 3.8 31.2 - - + -
386B PHE* 4.2 11.9 - - + -
388B ILE* 4.1 19.7 - - + -
397B ALA 3.3 17.0 - - - +
398B GLY* 4.0 0.2 - - - -
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Residues in contact with TYR 321 (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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161B TYR* 5.7 3.1 - + - -
320B VAL* 1.3 75.6 - - - +
322B ILE* 1.3 80.6 + - - +
323B LEU* 3.6 19.3 - - + -
324B LYS* 3.6 17.2 - - - +
327B GLU* 2.4 39.5 + - - -
365B GLY* 3.8 8.3 - - - -
366B ASP 3.5 4.0 - - - -
367B ASN* 3.2 35.2 - - - +
396B GLY* 3.0 5.9 - - - -
397B ALA* 2.7 45.2 + - + +
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Residues in contact with ILE 322 (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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320B VAL* 4.1 14.6 - - + -
321B TYR* 1.3 90.8 - - - +
323B LEU* 1.3 63.0 + - - +
330B ARG* 5.4 8.5 - - + -
334B PHE* 3.9 29.4 - - + -
362B VAL* 3.7 20.6 - - + -
363B MET 3.8 9.2 - - - +
364B PRO* 3.7 24.2 - - + -
365B GLY* 2.9 21.5 + - - -
366B ASP 2.8 16.9 + - - +
368B VAL* 4.3 7.2 - - + -
370B PHE* 4.9 3.6 - - + -
388B ILE* 4.9 4.5 - - + -
395B VAL* 3.4 17.7 - - + +
396B GLY* 4.2 3.6 - - - -
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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