Contacts of the strand formed by residues 355 - 363 (chain D) in PDB entry 1F6A
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 355 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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342D ARG 4.9 0.5 - - - -
343D PRO* 4.1 14.6 - - - +
347D ASP* 5.2 7.2 + - - +
353D SER* 4.0 8.7 + - - +
354D PRO* 1.3 82.2 - - - +
356D ILE* 1.3 64.1 + - - +
357D THR* 4.3 3.5 + - - -
402D THR* 3.7 21.5 - - + +
403D LEU 3.2 16.4 - - - +
404D PRO* 3.7 17.0 - - + -
405D VAL* 4.6 1.6 - - - +
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Residues in contact with ILE 356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340D LEU* 4.8 4.5 - - + -
341D SER 3.4 13.7 - - - +
342D ARG* 4.4 0.7 - - - -
343D PRO* 3.4 35.0 - - + -
355D THR* 1.3 70.5 - - - +
357D THR* 1.3 65.4 + - - +
374D TRP* 3.7 25.2 - - + -
401D SER 4.2 0.5 - - - +
402D THR* 3.5 1.0 - - - +
403D LEU* 2.9 39.0 + - + +
405D VAL* 4.4 12.7 - - + +
410D TRP* 4.2 10.5 - - + -
416D TYR* 3.7 37.0 - - + -
433D THR* 4.7 8.5 - - + -
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Residues in contact with THR 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339D TYR 3.9 0.5 - - - +
340D LEU* 3.3 6.9 - - - -
341D SER* 2.8 45.7 + - - -
355D THR* 4.4 3.5 + - - -
356D ILE* 1.3 78.8 + - - +
358D CYS* 1.3 69.4 + - - +
359D LEU* 3.9 4.8 + - + +
400D THR* 4.7 9.0 - - - -
401D SER 3.5 9.6 - - - +
402D THR* 3.5 28.8 + - - +
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Residues in contact with CYS 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338D ALA* 5.2 4.5 - - - -
339D TYR 3.4 11.7 - - - -
340D LEU* 3.8 4.0 - - + +
357D THR* 1.3 72.6 - - - +
359D LEU* 1.3 61.6 + - - +
360D VAL* 4.8 5.6 - - - +
372D LEU* 4.6 5.5 - - + +
374D TRP* 3.6 18.8 - - + -
399D VAL 3.9 1.2 - - - +
400D THR* 3.4 3.1 - - - -
401D SER* 2.9 33.4 + - - +
418D CYS* 2.0 49.4 - - - -
420D VAL* 4.6 9.0 - - - -
431D ARG* 5.8 1.8 - - - -
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Residues in contact with LEU 359 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338D ALA* 3.5 2.1 - - - -
339D TYR* 2.9 48.3 + - + +
357D THR* 3.9 6.4 + - + +
358D CYS* 1.3 73.0 - - - +
360D VAL* 1.3 69.9 + - - +
361D VAL* 4.0 14.1 - - + -
398D THR* 3.3 30.1 - - + -
399D VAL 3.6 0.9 - - - -
400D THR* 3.5 17.7 - - + +
2H NAG 4.2 32.3 - - + +
3H MAN 4.2 18.2 - - - -
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Residues in contact with VAL 360 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336D VAL* 3.7 21.3 - - + -
337D SER 3.5 3.4 - - - +
338D ALA* 4.4 7.0 - - + -
358D CYS* 4.8 3.4 - - - +
359D LEU* 1.3 74.3 - - - +
361D VAL* 1.3 66.7 + - - +
363D LEU* 3.7 29.2 - - + -
370D VAL* 5.8 1.1 - - + -
372D LEU* 4.3 12.6 - - + -
398D THR* 3.3 9.9 - - - +
399D VAL* 2.8 44.2 + - + +
420D VAL* 3.7 33.7 - - + -
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Residues in contact with VAL 361 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336D VAL* 3.3 5.9 - - - +
337D SER* 2.9 36.1 + - - +
339D TYR* 3.7 31.4 - - + +
359D LEU* 4.0 16.4 - - + -
360D VAL* 1.3 79.5 - - - +
362D ASP* 1.3 92.3 + - + +
363D LEU 3.2 4.1 + - - +
397D LEU 4.6 0.9 - - - -
398D THR* 4.5 9.0 - - - +
1H NAG 4.3 13.9 - - - +
2H NAG 4.4 17.9 - - - +
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Residues in contact with ASP 362 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D CPS 5.0 3.5 + - - +
334D ARG* 3.4 42.1 + - - +
335D GLY 3.4 21.7 - - - +
336D VAL* 3.8 8.4 + - - +
337D SER* 3.6 3.6 + - - -
361D VAL* 1.3 91.8 - - - +
363D LEU* 1.3 65.2 + - - +
364D ALA* 4.9 2.3 - - - +
396D THR* 3.0 19.3 + - - +
397D LEU 4.1 1.6 + - - -
398D THR* 5.2 0.2 + - - -
1H NAG 3.2 33.1 + - - +
2H NAG 5.4 1.0 + - - -
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Residues in contact with LEU 363 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336D VAL* 3.2 23.3 - - + -
360D VAL* 3.7 25.4 - - + -
361D VAL 3.2 2.6 - - - -
362D ASP* 1.3 79.1 - - - +
364D ALA* 1.3 61.4 + - - +
370D VAL* 3.9 32.5 - - + -
396D THR* 3.1 7.4 + - - -
397D LEU* 3.0 48.3 + - + +
399D VAL* 3.4 33.7 - - + +
420D VAL* 6.2 1.3 - - + -
422D HIS* 4.3 17.5 - - + -
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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