Contacts of the strand formed by residues 377 - 381 (chain A) in PDB entry 1SLL
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 VAL 377 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376A PRO* 1.3 80.9 - - - +
378A LEU* 1.3 66.2 + - - +
388A PHE 3.6 0.7 - - - +
389A LEU* 3.5 7.1 - - - +
390A PHE* 2.9 49.8 + - + +
539A VAL* 3.7 27.4 - - + -
540A GLY 3.5 23.1 - - - +
541A PRO* 4.0 0.4 - - + -
542A GLY 3.2 4.3 - - - +
543A ILE 3.6 7.0 - - - +
544A GLY* 3.5 27.6 - - - +
558A VAL* 4.2 14.4 - - + -
559A PRO* 5.1 0.9 - - + -
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Residues in contact with LEU 378 (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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296A SER* 3.2 23.1 - - - +
297A LEU 4.6 0.7 - - - +
298A LEU* 4.0 16.8 - - + +
306A ILE* 4.1 27.1 - - + +
307A SER* 3.8 35.2 - - - -
308A ALA* 3.8 7.4 - - + +
327A PHE* 4.4 11.4 - - + -
377A VAL* 1.3 74.6 - - - +
379A LEU* 1.3 61.6 + - - +
387A ILE* 5.5 0.4 - - + -
388A PHE 3.5 13.5 - - - +
389A LEU* 3.8 22.9 - - + -
520A TRP* 4.9 2.2 - - + -
542A GLY 3.1 6.7 + - - -
543A ILE* 3.1 9.9 - - + +
544A GLY 2.9 22.4 + - - -
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Residues in contact with LEU 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A LEU* 3.9 9.1 - - + +
306A ILE* 5.6 0.2 - - - +
377A VAL* 5.2 0.2 - - + -
378A LEU* 1.3 77.8 - - - +
380A GLU* 1.3 77.4 + - - +
387A ILE* 3.2 5.5 - - - +
388A PHE* 2.7 41.3 + - + -
390A PHE* 4.2 16.6 - - + -
544A GLY* 3.4 9.9 - - - +
545A LYS* 3.4 32.8 - - - +
546A GLN* 4.2 2.5 - - + +
556A LEU* 3.9 28.5 - - + -
557A LEU 3.9 18.4 - - - +
558A VAL* 4.2 12.6 - - + -
580A TRP* 4.6 2.5 - - + -
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Residues in contact with GLU 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A LEU* 4.0 7.0 - - + +
299A THR 4.4 0.9 - - - +
300A LEU* 3.4 28.1 - - + +
301A SER* 2.6 47.6 + - - -
302A THR* 5.4 1.0 - - - +
379A LEU* 1.3 91.7 - - - +
381A ASP* 1.3 66.9 + - - +
382A LYS* 3.4 28.3 + - + +
385A LYS* 3.8 16.5 - - - +
386A ARG 3.3 10.5 - - - +
387A ILE* 4.2 7.9 - - + +
388A PHE* 4.8 0.9 - - - -
546A GLN* 3.8 11.1 + - - +
556A LEU* 4.5 0.4 - - - +
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Residues in contact with ASP 381 (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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380A GLU* 1.3 72.5 - - - +
382A LYS* 1.3 52.7 + - - +
383A LEU* 3.0 20.6 + - - +
384A THR* 3.3 20.6 + - - +
385A LYS* 2.6 36.2 + - - -
386A ARG 2.8 13.3 + - - +
388A PHE* 3.9 16.0 - - + -
546A GLN* 3.1 20.6 - - - +
556A LEU* 4.0 5.9 - - + +
576A HIS* 2.7 41.3 - - - +
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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
------------------------------------------------------------
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