Contacts of the strand formed by residues 355 - 363 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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342B ARG 4.9 0.5 - - - -
343B PRO* 4.0 15.5 - - - +
347B ASP* 5.2 7.3 + - - +
353B SER* 4.0 8.5 + - - +
354B PRO* 1.3 86.0 - - - +
356B ILE* 1.3 65.3 + - - +
357B THR* 4.3 3.3 + - - -
402B THR* 3.7 21.6 - - + +
403B LEU 3.2 16.2 - - - +
404B PRO* 3.6 16.4 - - + -
405B VAL* 4.5 1.6 - - - +
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Residues in contact with ILE 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B LEU* 4.8 6.1 - - + -
341B SER 3.4 13.2 - - - +
342B ARG* 4.4 0.7 - - - -
343B PRO* 3.3 35.2 - - + -
355B THR* 1.3 72.2 - - - +
357B THR* 1.3 64.2 + - - +
374B TRP* 3.7 30.1 - - + -
401B SER 4.1 0.5 - - - +
402B THR* 3.4 0.7 - - - +
403B LEU* 2.8 40.0 + - + +
405B VAL* 4.4 10.8 - - + -
410B TRP* 4.2 11.0 - - + -
416B TYR* 3.7 32.1 - - + -
433B THR* 4.7 6.5 - - + -
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Residues in contact with THR 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B TYR 3.5 1.9 - - - +
340B LEU* 3.3 6.5 - - - -
341B SER* 2.8 43.7 + - - -
355B THR* 4.4 3.5 + - - -
356B ILE* 1.3 80.2 + - - +
358B CYS* 1.3 68.0 + - - +
359B LEU* 3.9 4.6 + - + +
400B THR* 4.7 9.2 - - + -
401B SER 3.5 10.3 - - - +
402B THR* 3.5 29.9 + - - +
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Residues in contact with CYS 358 (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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338B ALA* 5.1 6.7 - - - -
339B TYR 3.3 7.9 - - - -
340B LEU* 3.8 5.6 - - + +
357B THR* 1.3 73.6 - - - +
359B LEU* 1.3 60.7 + - - +
360B VAL* 4.8 5.5 - - - +
372B LEU* 4.6 5.5 - - + +
374B TRP* 3.6 18.6 - - + -
399B VAL 3.8 1.4 - - - +
400B THR* 3.4 2.9 - - - -
401B SER* 2.8 35.8 + - - +
418B CYS* 2.0 50.3 - - - -
420B VAL* 4.6 8.7 - - - -
431B ARG* 5.8 2.0 - - - -
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Residues in contact with LEU 359 (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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338B ALA* 3.1 3.7 - - - -
339B TYR* 2.6 50.4 + - + +
357B THR* 3.9 5.4 + - + +
358B CYS* 1.3 74.5 - - - +
360B VAL* 1.3 65.0 + - - +
361B VAL* 4.0 13.9 - - + -
398B THR* 3.3 33.4 - - + -
399B VAL 3.6 0.9 - - - -
400B THR* 3.5 19.1 - - + +
2G NAG 3.8 33.2 - - + +
3G MAN 4.7 14.8 - - - +
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Residues in contact with VAL 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B VAL* 3.8 17.5 - - + -
337B SER 3.7 4.3 - - - +
338B ALA* 4.2 7.6 - - + -
358B CYS* 4.8 3.1 - - - -
359B LEU* 1.3 75.0 - - - +
361B VAL* 1.3 65.6 + - - +
363B LEU* 3.6 31.9 - - + -
370B VAL* 5.9 1.8 - - + -
372B LEU* 4.4 11.9 - - + -
398B THR* 3.3 9.9 - - - +
399B VAL* 2.8 44.5 + - + +
420B VAL* 3.7 35.9 - - + -
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Residues in contact with VAL 361 (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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336B VAL* 3.5 6.9 - - - +
337B SER* 2.9 34.2 + - - +
339B TYR* 3.8 29.8 - - + -
359B LEU* 4.0 15.0 - - + -
360B VAL* 1.3 80.1 - - - +
362B ASP* 1.3 91.5 + - - +
363B LEU 3.3 4.0 + - - -
397B LEU 4.6 0.9 - - - -
398B THR* 4.5 9.0 - - - +
1G NAG 4.5 12.3 - - - +
2G NAG 4.5 19.5 - - + +
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Residues in contact with ASP 362 (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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117A LYS* 3.4 29.7 + - - -
129A TYR* 2.8 25.7 + - - +
131A TYR* 3.7 9.0 - - - -
154A LYS* 5.7 0.5 + - - -
336B VAL* 3.8 10.7 - - - +
337B SER* 3.9 5.2 + - - -
361B VAL* 1.3 90.8 - - - +
363B LEU* 1.3 64.5 + - - +
396B THR* 3.1 19.0 + - - +
397B LEU 4.1 1.2 + - - -
398B THR* 5.2 0.2 + - - -
1G NAG 3.1 39.9 + - - +
2G NAG 5.4 1.0 + - - -
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Residues in contact with LEU 363 (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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129A TYR* 4.0 1.4 - - - -
131A TYR* 4.8 4.9 - - - +
336B VAL* 3.9 24.9 - - + -
360B VAL* 3.6 24.9 - - + -
361B VAL 3.3 0.2 - - - -
362B ASP* 1.3 78.4 - - - +
364B ALA* 1.3 63.0 + - - +
370B VAL* 3.7 25.1 - - + -
396B THR* 3.1 7.1 + - - -
397B LEU* 3.1 47.6 + - + +
399B VAL* 3.5 32.8 - - + +
420B VAL* 6.2 1.3 - - + -
422B HIS* 5.3 6.5 - - - +
425B LEU* 5.1 10.3 - - + -
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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