Contacts of the strand formed by residues 676 - 685 (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 GLY 676 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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666A SER 3.6 3.8 - - - -
667A PRO* 3.9 0.9 - - - -
674A LYS 3.5 1.4 - - - -
675A ASN* 1.3 77.4 + - - +
677A LYS* 1.3 63.2 + - - +
703A ALA* 3.9 0.7 - - - -
704A VAL* 3.2 27.0 + - - +
705A ASP 4.7 1.0 + - - +
709A MET 4.7 0.4 + - - -
711A TYR* 3.2 46.7 - - - +
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Residues in contact with LYS 677 (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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664A LEU 3.6 1.0 - - - +
665A SER* 3.3 5.9 + - - -
666A SER 3.0 31.7 + - - +
668A ASN* 3.0 34.1 - - + +
675A ASN* 3.7 27.7 + - - +
676A GLY* 1.3 80.4 - - - +
678A ILE* 1.3 64.8 + - - +
679A TRP* 3.7 30.7 - - + +
701A SER* 4.5 13.1 + - - -
702A TYR 3.2 13.9 - - - +
703A ALA* 3.9 16.4 - - + +
704A VAL* 5.3 0.2 - - - -
711A TYR* 4.5 1.4 - - - -
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Residues in contact with ILE 678 (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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663A ILE* 3.5 30.5 - - + -
664A LEU 3.2 5.4 - - - +
665A SER* 4.7 6.1 - - - -
677A LYS* 1.3 76.1 - - - +
679A TRP* 1.3 60.4 + - - +
680A ILE* 4.5 1.1 + - - +
700A TYR 4.5 0.2 - - - -
701A SER* 3.4 1.7 + - - -
702A TYR* 2.7 45.3 + - + +
704A VAL* 4.3 13.0 - - + -
711A TYR* 4.5 10.5 - - - +
716A LEU* 4.8 8.1 - - + -
724A VAL* 5.4 2.5 - - + -
726A LEU* 4.4 12.3 - - + -
750A TYR* 3.9 33.4 - - + -
755A LEU* 4.0 27.7 - - + +
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Residues in contact with TRP 679 (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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637A GLY 3.7 18.6 - - - -
638A ILE* 3.8 33.0 - - + +
663A ILE* 3.3 8.0 - - - +
664A LEU* 2.7 51.4 + - + +
666A SER* 5.2 3.4 + - - -
668A ASN* 4.0 22.2 + - - +
677A LYS* 3.7 32.8 + - + +
678A ILE* 1.3 78.8 - - - +
680A ILE* 1.3 62.5 + - - +
681A GLY 4.1 0.2 - - - -
698A TRP* 3.8 36.7 - - + -
700A TYR 3.1 20.0 - - - +
701A SER* 3.5 24.7 - - - -
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Residues in contact with ILE 680 (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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656A ILE* 3.8 26.9 - - + -
661A ALA* 4.2 2.0 - - + -
662A ILE 3.5 7.0 - - - +
663A ILE* 4.4 14.8 - - + -
678A ILE* 5.4 0.7 - - + +
679A TRP* 1.3 77.8 - - - +
681A GLY* 1.3 61.3 + - - +
682A LEU* 3.8 23.0 + - + +
697A GLU 3.7 0.3 - - - +
698A TRP* 3.6 3.5 - - - -
699A LYS* 3.2 24.3 + - - +
700A TYR* 3.1 25.4 + - + -
752A ILE* 4.7 3.4 - - + -
755A LEU* 3.7 31.9 - - + +
756A THR* 3.6 28.7 - - + -
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Residues in contact with GLY 681 (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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661A ALA* 3.2 4.3 - - - -
662A ILE* 2.8 44.1 + - - +
680A ILE* 1.3 74.1 - - - +
682A LEU* 1.3 63.5 + - - -
683A VAL 3.9 0.2 + - - -
696A VAL* 3.6 13.0 - - - -
697A GLU 3.3 7.6 - - - -
698A TRP* 3.5 20.4 - - - -
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Residues in contact with LEU 682 (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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656A ILE* 3.8 23.1 - - + +
657A ASP* 3.8 29.4 - - + +
659A LYS* 4.0 26.2 - - + +
660A PRO 3.5 2.2 - - - -
661A ALA* 4.0 8.7 - - + -
680A ILE* 3.8 22.7 - - + +
681A GLY* 1.3 79.0 - - - +
683A VAL* 1.3 62.6 + - - +
684A ASN* 3.5 4.8 + - - +
696A VAL* 3.3 3.3 - - - -
697A GLU* 2.8 47.3 + - + +
699A LYS* 3.9 22.9 - - + +
700A TYR* 5.0 2.5 - - + -
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Residues in contact with VAL 683 (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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600A GLU 6.0 0.2 - - - +
601A MET* 4.0 31.0 - - + -
602A PRO* 4.0 13.0 - - + -
659A LYS* 4.0 6.1 - - - +
660A PRO* 2.9 49.9 + - + +
661A ALA 4.6 1.1 - - - +
662A ILE* 4.6 12.6 - - + -
681A GLY 4.7 2.5 - - - +
682A LEU* 1.3 71.4 - - - +
684A ASN* 1.3 66.6 + - - +
685A ASP 4.4 0.3 + - - -
694A TYR* 3.6 30.3 - - + -
695A SER 3.7 3.4 - - - +
696A VAL* 4.4 9.6 - - + -
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Residues in contact with ASN 684 (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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659A LYS* 2.7 37.4 + - - +
682A LEU 3.5 15.0 + - - -
683A VAL* 1.3 74.4 - - - +
685A ASP* 1.3 63.6 + - - +
686A THR* 3.7 2.9 + - + -
694A TYR* 3.2 9.6 - - - -
695A SER* 2.8 48.0 + - - +
697A GLU* 3.9 19.8 + - - +
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Residues in contact with ASP 685 (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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683A VAL 4.4 0.4 + - - -
684A ASN* 1.3 72.4 - - - +
686A THR* 1.3 60.9 + - - +
687A GLY* 3.0 23.2 + - - -
693A LYS* 3.1 43.3 + - - +
694A TYR* 3.9 16.6 - - + -
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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