Contacts of the strand formed by residues 606 - 610 (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 LEU 606 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545A LYS* 4.5 6.3 - - + -
547A ILE* 4.2 17.5 - - + -
557A LEU* 4.0 32.1 - - + -
598A ILE* 4.3 14.1 - - + -
599A VAL 3.5 12.3 - - - +
600A GLU* 3.9 18.6 - - + -
601A MET* 4.7 0.4 - - - +
604A GLY 4.1 6.7 - - - +
605A SER* 1.3 84.7 - - - +
607A LYS* 1.3 64.2 + - - +
621A THR* 3.3 8.5 - - - +
622A SER 2.9 33.8 + - - +
625A GLY* 4.2 2.0 - - - -
626A GLY 4.1 17.9 - - - +
629A TRP* 3.9 19.1 - - + -
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Residues in contact with LYS 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A GLN 4.2 0.3 - - - +
598A ILE* 3.8 1.7 - - - +
599A VAL* 3.0 42.4 + - + +
601A MET* 3.7 35.5 - - + +
606A LEU* 1.3 77.5 - - - +
608A THR* 1.3 61.6 - - - +
609A TYR* 3.7 25.7 + - + +
619A GLU* 3.6 22.3 + - - +
620A VAL 3.4 5.4 - - - +
621A THR* 3.2 28.5 + - + +
691A ILE 4.1 6.7 + - - -
694A TYR* 3.5 32.0 + - - +
695A SER* 5.3 0.7 - - - +
696A VAL* 4.4 8.3 - - + -
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Residues in contact with THR 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A LEU* 4.6 1.1 - - + -
570A PHE* 3.5 22.3 - - + -
596A ALA* 3.5 25.1 - - + -
597A GLN 3.4 13.7 - - - +
598A ILE* 3.7 8.6 - - + +
607A LYS* 1.3 73.9 - - - +
609A TYR* 1.3 64.8 + - - +
610A LEU* 3.9 3.0 - - + +
618A ALA 3.8 0.2 - - - +
619A GLU* 3.3 5.4 - - - +
620A VAL* 2.8 49.6 + - + +
629A TRP* 3.1 24.6 - - - -
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Residues in contact with TYR 609 (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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596A ALA* 3.2 2.3 - - - -
597A GLN 3.1 29.7 + - - -
599A VAL* 3.8 24.0 - - + -
607A LYS* 3.7 25.9 - - + +
608A THR* 1.3 73.4 - - - +
610A LEU* 1.3 60.8 + - - +
617A ILE* 4.4 4.7 - - + -
618A ALA 3.3 7.2 - - - +
619A GLU* 3.2 33.1 + - + +
635A LEU* 3.8 31.0 - - + -
647A LEU* 3.9 23.3 - - + +
649A VAL* 3.8 21.8 - - + -
662A ILE* 3.9 8.9 - - + +
664A LEU* 4.7 3.8 - - + -
696A VAL* 3.7 18.7 - - - +
698A TRP* 4.0 14.4 + + - -
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Residues in contact with LEU 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A LEU* 4.1 23.8 - - + -
594A ALA* 4.1 8.7 - - + +
595A GLU 3.3 6.7 - - - +
596A ALA* 3.4 17.5 - - + -
608A THR* 3.9 13.2 - - + +
609A TYR* 1.3 74.1 - - - +
611A ARG* 1.3 76.3 + - - +
612A THR* 4.3 3.4 - - + -
617A ILE* 3.4 6.5 - - - +
618A ALA* 2.8 57.0 + - + +
619A GLU 4.4 0.2 - - - +
620A VAL* 4.1 11.2 - - + -
632A ARG* 3.8 36.1 - - - +
647A LEU* 4.0 7.2 - - - -
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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
------------------------------------------------------------
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