Contacts of the strand formed by residues 394 - 403 (chain F) in PDB entry 1TYE
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 THR 394 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69F LEU* 3.7 22.4 - - + -
103F GLN* 4.4 14.4 - - + +
104F VAL 3.2 13.9 - - - +
105F ARG* 2.7 33.2 + - - +
374F CYS 5.2 3.5 - - - +
375F LEU* 5.5 2.9 - - - +
377F ASN* 5.7 2.9 + - - -
392F GLY 3.5 3.0 + - - -
393F ASP* 1.3 74.5 - - - +
395F VAL* 1.3 70.8 + - - +
396F SER* 6.1 0.2 - - - -
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Residues in contact with VAL 395 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F GLN* 3.4 2.1 - - - +
104F VAL* 2.6 45.0 + - + +
355F VAL* 4.9 8.3 - - + -
373F THR 3.5 8.5 - - - +
374F CYS* 4.2 15.0 - - - -
375F LEU* 4.3 4.0 - - + +
386F CYS* 3.4 39.5 - - + -
389F LEU* 3.7 26.5 - - + -
393F ASP 4.4 0.2 + - - -
394F THR* 1.3 80.0 - - - +
396F SER* 1.3 61.7 + - - +
397F PHE* 3.8 20.5 - - + -
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Residues in contact with SER 396 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101F SER* 5.6 1.3 - - - -
102F ILE 3.3 10.8 - - - -
103F GLN* 3.7 17.3 - - - -
372F ALA* 3.8 0.2 - - - -
373F THR* 2.8 54.0 + - - +
377F ASN* 5.9 0.2 + - - -
394F THR* 6.1 0.4 - - - -
395F VAL* 1.3 77.3 - - - +
397F PHE* 1.3 68.3 + - - +
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Residues in contact with PHE 397 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101F SER* 3.8 5.4 + - - -
102F ILE* 2.8 49.1 + - + +
104F VAL* 4.3 10.3 - - + -
355F VAL* 3.8 37.0 - - + -
357F LEU* 3.4 35.2 - - + -
370F PHE* 5.1 3.8 - + + -
371F ASN 3.4 6.7 - - - -
372F ALA* 3.6 29.6 - - + -
373F THR* 6.1 0.2 - - - -
383F LEU 4.8 0.2 - - - -
384F LYS* 3.7 24.0 - - + -
385F SER 4.0 0.7 - - - -
386F CYS* 4.4 4.3 - - - -
395F VAL* 3.8 22.0 - - + -
396F SER* 1.3 78.9 - - - +
398F SER* 1.3 62.6 + - - +
399F ILE* 4.5 2.9 - - + -
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Residues in contact with SER 398 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99F ASN* 5.0 3.1 + - - +
100F PHE 3.5 9.5 + - - -
101F SER* 5.5 0.7 - - - -
369F SER 3.6 0.5 - - - +
370F PHE* 3.5 4.9 - - - +
371F ASN* 2.7 43.7 + - - -
397F PHE* 1.3 77.3 - - - +
399F ILE* 1.3 62.0 + - - +
1015F NAG 4.7 9.5 - - - +
1020F NAG 2.7 25.5 + - - +
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Residues in contact with ILE 399 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99F ASN* 3.1 4.4 - - - +
100F PHE* 2.8 71.4 + - + +
102F ILE* 3.5 32.8 - - + -
357F LEU* 5.3 2.0 - - + -
368F LEU* 3.6 31.9 - - + -
369F SER 3.2 12.1 - - - +
370F PHE* 3.5 31.2 - - + -
397F PHE* 4.5 2.2 - - + -
398F SER* 1.3 79.1 - - - +
400F GLU* 1.3 64.0 + - - +
401F ALA 4.3 0.2 - - - -
416F ILE* 4.9 6.3 - - + -
425F LEU* 5.2 3.8 - - + -
1020F NAG 4.6 0.9 - - - -
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Residues in contact with GLU 400 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97F SER* 3.7 27.6 + - - -
98F LYS 3.4 17.5 - - - +
99F ASN* 4.2 8.8 - - + +
367F SER 3.7 0.3 - - - +
368F LEU* 3.3 9.3 - - - -
369F SER* 3.0 39.9 + - - -
399F ILE* 1.3 76.0 - - - +
401F ALA* 1.3 61.5 + - - +
402F LYS* 4.1 3.9 + - + +
1020F NAG 3.3 37.6 + - + +
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Residues in contact with ALA 401 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90F LEU* 3.9 23.8 - - + -
92F LEU* 4.1 8.2 - - + +
96F ASP 4.0 0.2 - - - +
97F SER* 3.1 7.4 - - - -
98F LYS 2.9 34.4 + - - +
100F PHE* 4.5 5.8 - - + -
366F LEU* 3.8 14.1 - - + -
367F SER 3.5 5.4 - - - -
368F LEU* 3.6 14.8 - - + -
399F ILE 4.3 0.6 - - - -
400F GLU* 1.3 72.9 - - - +
402F LYS* 1.3 61.3 + - - +
414F PHE* 5.6 1.1 - - + -
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Residues in contact with LYS 402 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92F LEU* 4.9 0.2 - - - -
95F ASP* 4.2 16.6 + - - +
96F ASP 3.5 9.2 - - - +
97F SER* 3.3 21.1 - - - +
366F LEU* 3.3 2.8 - - - +
367F SER* 3.0 46.2 + - - +
400F GLU* 5.2 4.3 - - - +
401F ALA* 1.3 75.2 - - - +
403F VAL* 1.3 81.5 + - - +
404F ARG* 4.2 7.7 + - - +
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Residues in contact with VAL 403 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92F LEU* 3.4 36.1 - - + +
93F ARG 3.8 4.9 - - - +
94F PRO* 4.3 1.3 - - + -
95F ASP* 3.3 39.8 - - - +
96F ASP 3.6 3.7 + - - +
365F GLU 3.6 6.1 - - - +
366F LEU* 3.7 21.5 - - + -
402F LYS* 1.3 85.2 + - - +
404F ARG* 1.3 60.6 + - - +
405F GLY 3.4 11.8 + - - +
406F CYS* 5.8 1.1 - - - -
407F PRO* 5.9 0.4 - - + -
431F PHE* 3.6 26.2 - - + -
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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