Contacts of the strand formed by residues 343 - 347 (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 SER 343 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341H PRO 3.8 2.2 + - - -
342H PRO* 1.3 73.1 - - - +
344H VAL* 1.3 59.0 + - - +
345H TYR* 3.4 34.5 + - - -
364H LEU 3.6 2.6 - - - +
365H VAL* 3.7 0.7 - - - -
366H LYS* 2.9 39.5 + - - +
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Residues in contact with VAL 344 (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* 3.7 12.3 + - + +
343H SER* 1.3 75.6 - - - +
345H TYR* 1.3 68.2 + - - +
346H PRO* 4.0 0.2 - - - +
363H CYS* 4.3 3.1 - - + -
364H LEU 3.4 6.3 - - - +
365H VAL* 4.6 3.1 - - + -
418H CYS* 4.0 18.8 - - - -
420H VAL* 3.8 38.1 - - + -
429H VAL* 3.3 32.3 - - + -
431H LYS* 3.2 38.7 + - + +
123L GLU* 4.2 1.2 - - - +
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Residues in contact with TYR 345 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343H SER* 3.4 34.8 + - - -
344H VAL* 1.3 80.1 - - - +
346H PRO* 1.3 64.8 - - - +
347H LEU* 4.1 2.8 - - + +
363H CYS* 3.2 6.9 - - - +
364H LEU* 2.8 67.7 + - + +
366H LYS* 4.5 11.7 - - + -
431H LYS* 4.4 1.6 - - - -
121L SER* 3.4 26.2 - - - +
123L GLU* 4.0 13.9 - - + -
124L GLN* 3.5 42.0 - - + +
127L SER* 3.9 19.1 + - - -
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Residues in contact with PRO 346 (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 4.0 0.4 - - - +
345H TYR* 1.3 88.0 - - + +
347H LEU* 1.3 63.1 + - - +
348H ALA* 3.9 2.6 + - + -
362H GLY 3.9 0.4 - - - +
363H CYS* 4.2 1.3 - - - -
431H LYS* 3.2 29.4 - - + -
432H LYS 3.7 11.2 - - - +
433H ILE* 3.6 24.9 - - + -
434H VAL 5.2 1.6 - - - +
436H ARG* 4.9 1.9 + - - -
121L SER* 3.6 24.1 - - - -
123L GLU* 3.5 24.7 - - - +
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Residues in contact with LEU 347 (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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345H TYR* 4.2 4.0 - - + +
346H PRO* 1.3 79.5 - - - +
348H ALA* 1.3 61.5 + - - +
361H LEU* 3.7 3.8 - - - -
362H GLY* 2.7 45.0 + - - +
363H CYS 3.7 21.8 - - - +
364H LEU* 3.9 20.6 - - + +
401H SER* 4.2 1.6 - - - +
433H ILE* 3.8 6.5 - - - +
436H ARG* 4.8 1.3 - - - +
118L PHE* 3.5 26.5 - - + -
119L PRO 4.7 7.9 - - - +
120L PRO* 6.0 0.2 - - + -
121L SER 5.4 4.5 - - - +
131L SER 5.9 1.6 - - - +
133L VAL* 4.0 40.2 - - + -
135L PHE* 4.1 9.2 - - + -
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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