Contacts of the strand formed by residues 374 - 378 (chain N) in PDB entry 1A14
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 TYR 374 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351N GLY* 5.0 0.2 - - - -
352N PHE* 3.5 9.0 + + - -
363N GLY* 3.2 24.6 + - - -
364N ARG* 3.2 25.4 - - - -
365N THR* 4.3 4.5 - - + -
366N ILE* 3.9 4.7 - - - +
373N GLY* 1.3 78.4 - - - +
375N GLU* 1.3 69.4 + - - +
376N MET* 4.1 10.5 - - - -
396N THR* 3.7 1.0 - - - +
397N ILE* 2.6 44.2 + - + -
398N VAL* 2.7 34.4 + - + +
404N SER* 4.2 6.7 - - - -
405N GLY 4.6 5.2 - - - -
407N SER* 2.8 37.3 + - - -
422N PHE* 4.5 2.9 - + - -
424N VAL* 3.9 29.8 - - + -
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Residues in contact with GLU 375 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327N ARG* 5.0 0.7 + - - -
362N LEU 3.8 0.3 - - - +
363N GLY* 3.2 4.9 - - - -
364N ARG* 2.8 87.5 + - + +
366N ILE* 4.5 25.7 - - + +
374N TYR* 1.3 79.9 - - - +
376N MET* 1.3 64.2 - - - +
377N LEU* 4.0 17.6 - - + +
395N GLN 3.6 11.2 - - - +
396N THR* 4.5 9.4 + - - +
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Residues in contact with MET 376 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97N TRP* 3.4 38.8 - - + +
352N PHE* 3.9 28.3 - - + -
354N TYR* 5.5 0.2 - - + -
361N TRP* 3.6 25.9 - - + -
362N LEU 3.3 10.3 - - - +
363N GLY* 3.5 19.3 - - - -
374N TYR* 4.1 5.6 - - - -
375N GLU* 1.3 73.8 - - - +
377N LEU* 1.3 62.0 + - - +
394N GLY* 3.4 2.3 - - - -
395N GLN* 2.8 38.4 + - + +
397N ILE* 3.5 20.4 - - + -
422N PHE* 3.7 13.9 - - + -
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Residues in contact with LEU 377 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321N VAL* 3.9 16.2 - - + -
361N TRP* 3.1 4.6 - - - -
362N LEU* 2.7 42.5 + - + +
364N ARG* 3.2 47.6 - - - +
375N GLU* 4.0 22.0 - - + +
376N MET* 1.3 78.8 - - - +
378N LYS* 1.3 60.5 + - - +
379N VAL* 3.6 11.9 + - + +
390N PRO* 3.9 23.8 - - + -
392N GLN 3.7 6.5 - - - +
394N GLY* 4.9 5.2 - - - -
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Residues in contact with LYS 378 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94N ILE 4.8 3.9 + - - +
95N ASN* 5.1 7.1 + - - -
358N VAL* 3.0 37.1 + - - +
359N ASN* 5.1 1.1 - - - +
360N THR 3.3 16.6 - - - +
361N TRP* 3.4 41.5 - - + +
377N LEU* 1.3 68.4 - - - +
379N VAL* 1.3 59.8 + - - +
380N PRO* 3.1 14.5 - - + +
391N THR* 2.9 39.1 + - + +
392N GLN* 3.0 31.2 + - + +
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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