Contacts of the strand formed by residues 393 - 403 (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 ARG 393 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118B GLU* 4.4 1.6 - - - +
328B GLY* 3.1 25.0 + - - +
329B GLY 3.8 18.2 + - - -
330B ARG* 4.6 4.7 - - - +
331B HIS* 4.9 13.5 + - - -
389B ARG* 2.9 13.0 - - - +
390B GLU 2.6 41.3 + - - +
391B GLY 3.3 5.3 + - - -
392B GLY* 1.3 83.2 - - - +
394B THR* 1.3 75.3 - - - +
395B VAL* 3.7 11.8 - - + +
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Residues in contact with THR 394 (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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118B GLU* 2.4 39.1 + - + +
121B LEU* 4.0 24.0 - - + -
122B LEU* 3.9 11.3 - - + +
323B LEU* 4.4 9.2 - - + +
328B GLY 3.8 3.6 + - - +
329B GLY* 3.6 13.3 + - - -
387B ALA* 4.9 0.4 - - + -
388B ILE 3.4 9.0 - - - +
389B ARG* 3.0 21.9 + - + +
393B ARG* 1.3 83.3 - - - +
395B VAL* 1.3 68.4 + - - +
396B GLY 4.0 11.7 - - - +
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Residues in contact with VAL 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B ILE* 3.4 15.3 - - + +
323B LEU* 2.8 32.5 + - - +
329B GLY* 4.7 1.6 - - - -
330B ARG* 4.1 28.9 - - + +
338B TYR* 4.4 20.4 - - + +
388B ILE* 2.5 40.0 + - + +
389B ARG* 4.1 2.9 - - - +
390B GLU* 4.2 8.5 - - - +
393B ARG* 3.7 22.2 - - + +
394B THR* 1.3 81.2 - - - +
396B GLY* 1.3 59.9 + - - +
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Residues in contact with GLY 396 (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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121B LEU* 4.8 0.7 - - - +
321B TYR 3.0 11.9 - - - -
322B ILE* 4.2 5.8 - - - -
323B LEU* 4.3 4.7 - - - -
387B ALA* 3.6 3.1 - - - +
388B ILE* 2.8 42.4 + - - +
394B THR* 4.0 7.6 - - - +
395B VAL* 1.3 85.2 - - - +
397B ALA* 1.3 59.6 + - - +
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Residues in contact with ALA 397 (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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121B LEU* 4.3 16.6 - - + -
125B GLN* 3.8 24.2 - - + +
320B VAL* 3.3 3.6 - - - +
321B TYR* 2.7 43.5 + - + +
323B LEU* 4.9 0.4 - - + -
386B PHE* 3.7 9.0 - - - -
387B ALA* 4.4 0.2 - - - +
396B GLY* 1.3 74.4 - - - +
398B GLY* 1.3 57.3 + - - +
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Residues in contact with GLY 398 (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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125B GLN* 3.1 10.8 + - - +
319B SER 3.2 14.4 - - - -
320B VAL* 4.0 2.2 - - - -
385B ARG* 3.3 3.1 - - - +
386B PHE* 2.9 45.7 + - - -
397B ALA* 1.3 74.2 - - - +
399B VAL* 1.3 61.9 + - - -
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Residues in contact with VAL 399 (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* 3.4 0.5 - - - -
319B SER* 3.2 34.8 + - - +
383B GLY* 3.2 39.5 - - - +
384B LEU 3.2 6.7 - - - +
385B ARG* 3.7 10.5 - - + +
386B PHE* 3.2 7.6 - - - -
398B GLY* 1.3 74.8 - - - +
400B VAL* 1.3 70.1 + - - +
401B THR* 3.0 8.2 + - - +
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Residues in contact with VAL 400 (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* 3.8 23.8 - - + -
317B GLU 3.9 4.3 - - - +
344B PHE* 4.3 7.2 - - + -
380B LEU* 4.0 23.3 - - + -
381B GLU 3.4 24.2 - - - +
382B GLU* 3.3 9.2 - - - -
383B GLY* 2.4 32.7 + - - -
384B LEU* 2.6 17.9 + - + +
386B PHE* 3.5 3.7 - - + -
399B VAL* 1.3 69.8 - - - +
401B THR* 1.3 61.0 + - - +
402B LYS 3.7 19.1 - - - +
403B ILE* 4.0 14.1 - - + -
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Residues in contact with THR 401 (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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317B GLU* 2.7 35.6 + - + +
318B ALA* 3.6 9.0 - - - +
319B SER* 3.5 22.0 + - - -
369B THR* 6.0 2.5 - - + -
382B GLU* 4.1 13.1 - - - +
399B VAL* 3.0 7.1 + - - +
400B VAL* 1.3 74.4 - - - +
402B LYS* 1.3 60.5 + - + +
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Residues in contact with LYS 402 (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* 2.9 7.8 - - - +
317B GLU* 2.9 53.9 + - + +
382B GLU* 3.6 17.5 - - - +
400B VAL* 3.6 2.8 - - - +
401B THR* 1.3 83.1 - - + +
403B ILE* 1.3 72.5 + - - +
404B LEU* 4.0 14.1 - - + -
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Residues in contact with ILE 403 (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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313B HIS* 3.1 48.0 - - + +
315B LYS 3.6 10.5 - - - +
316B PHE* 4.7 2.7 - - + -
380B LEU* 3.8 21.1 - - + +
381B GLU* 3.8 19.1 - - - +
382B GLU* 3.9 14.6 + - + +
400B VAL* 4.0 12.1 - - + -
402B LYS* 1.3 84.5 - - - +
404B LEU* 1.3 72.6 + - - +
405B GLU* 4.1 6.5 - - - +
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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