Contacts of the strand formed by residues 556 - 563 (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 556 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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379A LEU* 3.9 14.8 - - + -
380A GLU 4.5 1.6 - - - +
381A ASP* 4.0 11.9 - - + +
388A PHE* 4.0 16.6 - - + -
545A LYS 3.7 3.1 - - - -
546A GLN* 3.2 41.1 - - + +
554A GLY 3.6 3.8 - - - +
555A ARG* 1.3 72.3 - - - +
557A LEU* 1.3 61.2 + - - +
572A TYR* 3.0 8.1 - - - +
573A SER* 2.9 34.3 + - - +
576A HIS* 3.6 11.7 - - - -
577A GLY* 3.4 34.8 - - - +
580A TRP* 3.8 16.6 - - + -
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Residues in contact with LEU 557 (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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379A LEU* 3.9 1.8 - - - +
544A GLY* 3.3 5.4 - - - -
545A LYS* 2.7 50.8 + - + +
547A ILE* 3.6 32.8 - - + -
555A ARG* 3.8 5.2 - - + +
556A LEU* 1.3 81.2 - - - +
558A VAL* 1.3 65.0 + - - +
559A PRO* 4.2 1.4 - - - +
570A PHE* 5.0 11.4 - - + -
571A MET 3.4 4.7 - - - +
572A TYR* 4.0 13.2 - - + -
598A ILE* 4.2 14.3 - - + +
606A LEU* 4.0 18.2 - - + -
625A GLY 3.8 19.5 - - - +
626A GLY* 4.1 10.5 - - - +
629A TRP* 4.8 6.1 - - + -
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Residues in contact with VAL 558 (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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377A VAL* 4.2 24.9 - - + -
379A LEU* 4.2 9.2 - - + -
390A PHE* 3.6 35.9 - - + -
539A VAL* 4.5 3.8 - - + -
557A LEU* 1.3 80.3 - - - +
559A PRO* 1.3 81.0 - - + +
560A LEU* 3.7 6.3 - - + +
570A PHE* 3.4 5.3 - - - -
571A MET* 2.9 54.2 + - + -
580A TRP* 4.2 7.0 - - + -
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Residues in contact with PRO 559 (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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377A VAL* 5.1 0.9 - - + -
539A VAL* 3.5 0.9 - - - -
540A GLY* 2.9 35.5 + - - +
543A ILE 4.1 13.0 - - - +
544A GLY* 4.5 0.9 - - - -
557A LEU 4.2 1.3 - - - +
558A VAL* 1.3 89.7 - - + +
560A LEU* 1.3 67.6 + - - +
568A LEU* 5.5 0.2 - - + -
570A PHE* 3.9 16.6 - - + -
596A ALA* 3.4 37.0 - - + +
597A GLN* 3.7 7.9 - - - +
598A ILE* 3.7 24.2 - - + -
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Residues in contact with LEU 560 (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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508A LEU* 4.3 15.3 - - + -
529A PHE* 4.6 0.7 - - + -
537A LEU* 4.1 15.9 - - + -
538A VAL 3.1 14.6 - - - +
539A VAL* 4.1 12.8 - - + +
540A GLY* 4.2 1.1 - - - +
558A VAL* 3.7 20.2 + - + +
559A PRO* 1.3 94.9 - - - +
561A TYR* 1.3 67.2 + - - +
568A LEU* 3.5 9.2 - - - +
569A GLY 2.9 31.6 + - - +
570A PHE 3.8 23.6 - - - -
571A MET* 3.9 18.6 - - + -
582A TYR* 3.8 20.4 - - + -
594A ALA 4.2 1.5 - - - +
596A ALA* 5.8 0.2 - - - +
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Residues in contact with TYR 561 (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 ASP* 4.9 6.3 + - - -
400A SER* 5.8 1.6 + - - -
536A PHE* 3.8 18.3 - + - -
537A LEU* 3.5 2.7 - - - -
538A VAL* 2.8 57.6 + - + +
539A VAL 3.4 20.4 - - - -
540A GLY* 4.6 0.2 - - - -
541A PRO* 5.1 0.2 - - + -
560A LEU* 1.3 78.4 - - - +
562A SER* 1.3 64.2 + - - +
567A GLU 2.9 13.2 - - - +
569A GLY 4.4 0.2 - - - +
592A ALA 3.6 16.2 - - - -
593A THR* 3.3 32.6 - - + +
594A ALA* 3.6 24.0 - - + +
595A GLU* 3.6 31.1 + - + -
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Residues in contact with SER 562 (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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536A PHE* 2.9 31.4 - - - -
537A LEU* 3.7 13.6 - - - +
561A TYR* 1.3 79.2 - - - +
563A LYS* 1.3 56.9 + - - +
564A SER* 3.5 12.4 + - - -
566A ALA 2.8 31.8 + - - +
567A GLU* 2.7 20.2 + - - +
582A TYR* 3.8 11.6 + - - -
591A GLY* 3.4 15.8 - - - -
592A ALA 4.6 0.2 - - - +
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Residues in contact with LYS 563 (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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533A VAL 4.6 0.5 - - - +
534A SER* 3.3 1.4 - - - -
535A LYS* 2.9 51.1 + - + +
536A PHE* 3.2 32.0 + - + +
562A SER* 1.3 70.0 - - - +
564A SER* 1.3 60.3 + - - +
589A THR* 2.7 30.0 + - - +
590A GLY* 3.9 9.7 + - - +
591A GLY* 3.6 13.5 - - - -
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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