Contacts of the strand formed by residues 358 - 368 (chain H) in PDB entry 1FNS
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 MET 358 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357H SER* 1.3 85.6 + - - +
359H VAL* 1.3 61.2 + - - +
405H THR* 3.7 27.8 - - + +
406H VAL* 3.4 26.5 - - - +
407H PRO* 3.6 28.0 - - + -
408H SER* 3.9 5.2 + - - -
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Residues in contact with VAL 359 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349H PRO* 4.3 9.9 - - + -
358H MET* 1.3 76.3 - - - +
360H THR* 1.3 69.3 + - - +
361H LEU* 3.6 23.5 + - + -
404H VAL 3.7 0.7 - - - +
405H THR* 3.3 2.3 - - - -
406H VAL* 2.9 55.1 + - + +
407H PRO 4.4 3.8 - - - +
408H SER* 4.4 7.4 - - - +
411H TRP* 4.2 33.9 - - + +
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Residues in contact with THR 360 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349H PRO* 4.3 3.1 - - - +
358H MET 5.6 0.2 - - - -
359H VAL* 1.3 77.4 - - - +
361H LEU* 1.3 76.6 + - - +
403H SER* 4.1 16.4 - - - +
404H VAL 3.2 6.5 - - - +
405H THR* 2.6 31.0 + - - +
114L THR* 4.9 10.0 - - - +
116L SER* 3.6 26.4 + - - +
118L PHE* 3.4 22.1 - - + -
135L PHE* 4.4 3.1 - - + -
137L ASN* 4.4 7.6 + - - +
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Residues in contact with LEU 361 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347H LEU 3.7 5.4 - - - +
349H PRO* 3.6 24.0 - - + -
359H VAL* 3.6 13.7 - - + -
360H THR* 1.3 85.5 - - - +
362H GLY* 1.3 59.5 + - - +
377H TRP* 4.3 1.3 - - + -
403H SER* 3.2 6.4 - - - -
404H VAL* 2.8 39.6 + - + -
406H VAL* 4.5 11.9 - - + -
411H TRP* 3.8 37.5 - - + -
416H VAL* 4.0 24.7 - - + -
433H ILE* 3.7 21.8 - - + -
118L PHE* 4.2 5.8 - - - -
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Residues in contact with GLY 362 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347H LEU* 2.7 49.3 + - - +
361H LEU* 1.3 76.2 - - - +
363H CYS* 1.3 55.0 + - - -
377H TRP* 3.5 8.5 - - - -
402H SER 3.1 12.6 - - - -
403H SER* 4.0 1.6 - - - -
433H ILE* 3.4 12.5 - - - +
118L PHE* 4.4 0.2 - - - -
135L PHE* 4.1 3.6 - - - -
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Residues in contact with CYS 363 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344H VAL* 4.3 8.1 - - + -
345H TYR 3.2 12.1 - - - +
346H PRO* 4.2 2.7 - - - -
347H LEU* 3.7 4.4 - - - +
362H GLY* 1.3 76.4 - - - -
364H LEU* 1.3 59.3 + - - +
365H VAL* 3.9 9.1 + - + +
375H VAL* 5.4 0.7 - - + -
377H TRP* 3.8 4.5 - - + -
401H SER* 3.3 4.9 + - - -
402H SER* 2.9 33.4 + - - +
418H CYS* 2.0 53.2 - - + -
420H VAL* 5.3 0.7 - - + -
431H LYS* 4.4 1.8 - - - -
433H ILE* 3.8 13.7 - - - -
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Residues in contact with LEU 364 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343H SER 3.6 1.9 - - - +
344H VAL* 3.4 3.5 - - - +
345H TYR* 2.8 58.1 + - + +
347H LEU* 3.9 16.7 - - + +
363H CYS* 1.3 71.9 - - - +
365H VAL* 1.3 59.5 + - - +
366H LYS* 4.3 9.9 - - + -
399H THR* 3.8 26.7 - - + -
400H LEU 3.9 0.9 - - - +
401H SER* 3.5 20.2 - - - +
124L GLN* 4.1 7.2 - - - +
131L SER* 3.5 34.1 - - - +
133L VAL* 4.3 12.6 - - + -
178L THR* 4.7 10.1 - - + +
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Residues in contact with VAL 365 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342H PRO* 3.5 26.2 - - + -
343H SER 3.7 3.1 - - - -
344H VAL* 4.6 3.8 - - + +
363H CYS* 4.3 11.4 - - + +
364H LEU* 1.3 75.3 - - - +
366H LYS* 1.3 59.0 + - - +
368H TYR* 3.9 14.6 - - + -
373H VAL* 4.5 6.3 - - + -
375H VAL* 4.4 5.4 - - + -
399H THR* 3.3 3.7 - - - -
400H LEU* 2.8 60.5 + - + +
402H SER* 5.9 0.2 - - - -
420H VAL* 3.7 38.6 - - + -
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Residues in contact with LYS 366 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342H PRO* 3.5 1.6 - - - +
343H SER* 2.9 46.2 + - - +
345H TYR* 4.5 10.3 - - + +
364H LEU* 4.3 13.2 - - + -
365H VAL* 1.3 75.8 - - - +
367H GLY* 1.3 69.1 + - - +
368H TYR 3.6 2.0 - - - -
394H GLN* 2.7 36.7 + - - +
398H TYR 3.9 0.2 - - - -
399H THR* 3.5 16.4 - - + +
124L GLN* 4.0 25.6 - - - +
131L SER* 4.1 4.7 + - - +
180L THR* 3.8 24.7 + - - +
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Residues in contact with GLY 367 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340H THR* 3.5 22.5 - - - +
341H PRO 3.6 4.6 - - - +
366H LYS* 1.3 83.0 - - - +
368H TYR* 1.3 59.1 + - - +
397H LEU* 3.6 26.9 - - - +
398H TYR 3.1 9.6 + - - -
399H THR* 3.6 2.4 + - - -
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Residues in contact with TYR 368 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340H THR 3.2 13.0 - - - +
342H PRO* 3.7 33.2 - - + -
365H VAL* 3.9 25.1 - - + -
367H GLY* 1.3 76.7 - - - +
369H PHE* 1.3 67.2 + - - +
370H PRO 3.6 18.8 - - - -
371H GLU* 2.9 30.8 + - - -
373H VAL* 3.4 26.5 - - + +
391H ALA* 3.4 15.8 - - - +
397H LEU* 3.5 3.6 - - - -
398H TYR* 2.7 77.3 + - + -
399H THR* 4.2 1.8 - - - -
400H LEU* 3.5 5.4 - - + +
422H HIS* 4.0 5.8 - - - +
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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