Contacts of the strand formed by residues 393 - 403 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118C GLU* 4.4 2.5 - - - +
325C LYS 5.6 0.6 + - - -
328C GLY* 3.0 26.4 + - - +
329C GLY 3.7 15.5 + - - -
330C ARG* 4.8 4.9 - - - +
331C HIS* 5.7 6.6 + - - -
389C ARG* 3.1 12.0 - - - +
390C GLU 2.6 48.7 + - - +
391C GLY 4.4 6.6 + - - -
392C GLY* 1.3 82.3 - - - +
394C THR* 1.3 69.0 + - - +
395C VAL* 3.1 7.8 - - + +
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Residues in contact with THR 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C GLU* 2.8 22.5 + - + +
121C LEU* 4.2 20.4 - - + -
122C LEU* 3.9 12.1 - - + +
323C LEU* 4.2 11.1 - - + +
328C GLY 4.1 1.8 + - - +
329C GLY* 3.8 12.6 - - - -
387C ALA* 5.2 0.7 - - + -
388C ILE 3.2 11.4 - - - +
389C ARG* 2.8 33.1 + - + +
393C ARG* 1.3 76.9 - - - +
395C VAL* 1.3 71.3 + - - +
396C GLY 3.4 15.3 - - - +
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Residues in contact with VAL 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322C ILE* 3.4 11.8 - - + +
323C LEU* 2.9 29.9 + - - +
329C GLY* 4.8 2.9 - - - -
330C ARG* 4.6 23.0 + - + +
334C PHE* 5.5 4.0 - - + -
338C TYR* 4.1 22.7 - - + +
388C ILE* 2.6 35.0 + - + +
389C ARG* 4.4 2.0 - - - +
390C GLU* 3.6 16.2 - - + +
393C ARG* 3.1 25.8 - - + +
394C THR* 1.3 83.1 - - - +
396C GLY* 1.3 58.5 + - - +
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Residues in contact with GLY 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C LEU* 4.5 0.2 - - - +
321C TYR 3.1 15.3 - - - -
322C ILE* 4.1 4.0 - - - -
323C LEU* 4.3 3.8 - - - -
387C ALA* 4.1 1.0 - - - -
388C ILE* 3.1 39.1 + - - +
394C THR* 3.4 12.5 - - - +
395C VAL* 1.3 80.3 - - - +
397C ALA* 1.3 62.9 + - - +
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Residues in contact with ALA 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C LEU* 4.0 23.3 - - + -
124C ARG* 5.6 0.4 - - - +
125C GLN* 3.6 28.3 - - + +
320C VAL* 4.2 2.6 - - - +
321C TYR* 3.1 33.2 + - + +
323C LEU* 4.8 1.6 - - + -
386C PHE 3.6 9.2 - - - -
387C ALA* 4.3 2.0 - - - +
388C ILE* 4.0 3.0 - - - +
396C GLY* 1.3 75.0 - - - +
398C GLY* 1.3 58.8 + - - +
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Residues in contact with GLY 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C GLN* 3.1 10.1 + - - +
319C SER 3.3 15.0 - - - -
320C VAL* 4.2 3.6 - - - -
385C ARG* 3.6 1.7 - - - +
386C PHE* 3.0 45.7 + - - -
397C ALA* 1.3 74.4 - - - +
399C VAL* 1.3 61.2 + - - +
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Residues in contact with VAL 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318C ALA* 3.1 16.3 - - - +
319C SER* 3.1 28.9 + - - +
383C GLY* 3.2 28.7 - - - +
384C LEU 2.8 17.0 - - - +
385C ARG* 4.4 6.5 - - + +
386C PHE* 3.2 9.6 - - - -
398C GLY* 1.3 75.7 - - - +
400C VAL* 1.3 73.0 + - - +
401C THR* 3.2 4.4 + - - +
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Residues in contact with VAL 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316C PHE* 3.6 33.2 - - + -
317C GLU 4.1 1.8 - - - -
318C ALA* 4.2 0.9 - - - -
344C PHE* 4.2 18.6 - - + -
380C LEU* 4.7 7.4 - - + -
381C GLU 3.6 26.7 - - - +
382C GLU* 3.9 5.4 - - - -
383C GLY* 2.7 28.2 + - - -
384C LEU* 2.6 19.3 + - + +
386C PHE* 3.6 1.3 - - + -
399C VAL* 1.3 72.3 - - - +
401C THR* 1.3 62.6 + - - +
402C LYS 3.7 20.0 - - - +
403C ILE* 4.2 9.4 - - + -
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Residues in contact with THR 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C GLU* 2.8 38.7 + - + +
318C ALA* 3.7 10.8 - - - +
319C SER* 3.9 15.8 + - - -
369C THR* 6.1 1.8 - - + -
382C GLU* 4.2 14.1 - - - +
399C VAL* 3.2 5.2 + - - +
400C VAL* 1.3 77.4 + - - +
402C LYS* 1.3 66.6 + - + +
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Residues in contact with LYS 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316C PHE* 3.0 8.4 - - - +
317C GLU* 3.0 49.0 + - + +
382C GLU* 4.1 16.4 - - - +
400C VAL* 3.6 2.2 - - - +
401C THR* 1.3 84.7 - - + +
403C ILE* 1.3 75.7 + - - +
404C LEU* 4.1 16.6 - - + -
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Residues in contact with ILE 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313C HIS* 3.7 26.9 - - + +
315C LYS 3.4 12.3 - - - +
316C PHE* 4.1 2.0 - - + -
380C LEU* 3.3 46.4 - - + +
381C GLU* 3.6 8.3 - - - +
382C GLU* 4.3 15.3 + - + +
400C VAL* 4.2 9.0 - - + -
402C LYS* 1.3 86.7 - - - +
404C LEU* 1.3 73.2 + - - +
405C GLU* 3.6 13.7 - - - +
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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