Contacts of the strand formed by residues 373 - 377 (chain A) in PDB entry 1LAP
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 373 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364A MET* 4.7 0.7 - - - -
368A LEU* 4.7 0.4 - - - -
372A ALA* 1.3 76.1 - - - +
374A GLY* 1.3 66.2 + - - +
375A VAL* 4.3 0.3 - - - +
395A ASP* 4.7 4.9 - - - +
396A ARG 2.9 15.4 + - - +
397A VAL* 3.4 9.8 - - + +
398A TRP* 2.9 25.3 + - - +
448A LEU* 4.1 8.3 - - - +
449A ASP 3.9 4.9 - - - -
450A ILE* 3.2 26.8 - - - +
453A VAL* 3.9 20.6 - - + -
471A PRO* 3.6 31.8 - - + +
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Residues in contact with GLY 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364A MET* 3.5 26.3 - - - +
368A LEU* 4.3 1.6 - - - -
373A THR* 1.3 75.6 + - - +
375A VAL* 1.3 60.5 + - - +
376A PHE* 4.2 6.3 - - - -
398A TRP 3.4 7.4 - - - -
400A MET* 4.3 5.4 - - - -
448A LEU* 3.2 5.0 - - - -
449A ASP* 2.8 35.4 + - - +
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Residues in contact with VAL 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373A THR* 4.3 1.3 - - - +
374A GLY* 1.3 76.4 - - - +
376A PHE* 1.3 65.5 + - - +
377A THR* 3.9 24.9 - - + -
383A TRP* 3.2 35.2 - - + -
386A LEU* 5.2 7.4 - - + -
397A VAL* 4.2 11.7 - - + -
398A TRP 3.1 16.1 + - - +
399A ARG* 3.3 7.1 - - - +
400A MET* 2.6 32.2 + - - +
446A ALA* 4.4 5.2 - - + -
447A HIS 3.1 8.5 - - - +
448A LEU* 3.9 19.3 - - + -
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Residues in contact with PHE 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364A MET* 4.8 3.1 - - - -
374A GLY 4.7 1.8 - - - -
375A VAL* 1.3 76.2 - - - +
377A THR* 1.3 61.2 + - - +
400A MET* 3.4 38.4 - - + -
401A PRO 3.2 28.9 - - - -
402A LEU* 4.0 14.5 - - + +
429A ALA* 3.8 32.8 - - + -
430A CYS* 3.7 19.7 - - - -
433A ALA* 3.5 20.2 - - + -
445A TRP* 4.2 2.5 - - + +
446A ALA* 3.5 0.9 - - - -
447A HIS* 2.8 60.7 + + + +
449A ASP* 4.8 9.6 - - + -
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Residues in contact with THR 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375A VAL* 3.9 13.7 + - + -
376A PHE* 1.3 77.2 - - - +
378A ASN* 1.3 57.0 + - - +
379A SER* 2.9 29.3 + - - +
382A LEU* 3.9 7.4 - - - +
383A TRP* 3.7 22.7 - - + +
399A ARG* 2.9 37.7 + - - +
400A MET 4.8 1.6 + - - -
402A LEU* 3.8 14.0 - - - +
445A TRP* 2.8 21.3 + - - -
446A ALA* 4.0 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