Contacts of the strand formed by residues 622 - 626 (chain B) in PDB entry 1L8A
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 PHE 622 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578B TRP* 2.9 17.0 + - - +
593B ILE* 3.9 14.8 - - + -
594B PRO 3.0 12.1 + - - +
595B PHE* 3.2 51.1 - + + -
596B TYR 3.1 17.8 + - - -
621B GLY* 1.3 75.0 - - - -
623B LEU* 1.3 60.4 + - - +
624B ILE* 3.9 8.9 + - + -
670B MET* 3.7 25.8 - - + -
673B GLY* 4.2 0.7 - - - -
674B LEU* 3.6 22.7 - - + -
677B MET* 3.4 26.5 - - + -
687B TYR* 3.5 28.5 - + + +
689B ILE* 4.2 13.2 - - + -
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Residues in contact with LEU 623 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575B GLY* 6.2 0.7 - - - -
578B TRP* 3.1 49.6 - - + +
596B TYR* 3.8 16.8 - - + -
598B TYR* 4.1 10.1 - - + +
604B PHE* 4.1 18.2 - - + -
607B ILE* 6.1 3.6 - - + -
611B CYS* 4.4 12.3 - - - -
622B PHE* 1.3 72.4 - - - +
624B ILE* 1.3 62.9 + - - +
625B GLY 3.9 0.9 - - - -
686B TYR* 3.4 30.3 - - + -
687B TYR 2.7 14.6 + - - +
688B TYR* 3.3 14.1 - - + -
689B ILE 3.0 25.5 + - - -
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Residues in contact with ILE 624 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498B PHE* 3.7 38.1 - - + -
595B PHE* 4.6 1.8 - - + -
596B TYR 2.7 21.6 + - - +
597B ILE* 3.3 19.1 - - + -
598B TYR* 3.2 25.5 + - - -
622B PHE* 4.1 20.9 - - + +
623B LEU* 1.3 79.4 - - - +
625B GLY* 1.3 58.5 + - - +
626B GLY 3.1 6.9 + - - -
670B MET* 5.5 0.2 - - + -
689B ILE* 3.4 24.5 - - + +
691B THR* 3.7 34.5 - - + +
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Residues in contact with GLY 625 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598B TYR* 4.0 4.3 - - - -
600B SER* 3.6 22.4 - - - -
624B ILE* 1.3 69.4 - - - +
626B GLY* 1.3 64.1 + - - +
628B SER* 3.4 5.5 - - - -
688B TYR* 3.7 19.8 - - - -
689B ILE 2.9 11.3 + - - -
690B THR* 3.3 4.5 - - - -
691B THR* 2.9 24.5 + - - +
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Residues in contact with GLY 626 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495B THR* 4.7 0.4 - - - -
526B PHE* 3.8 14.6 - - - -
597B ILE* 4.5 2.5 - - - -
598B TYR 2.8 16.5 + - - +
600B SER* 2.9 15.6 + - - -
624B ILE 3.1 5.3 + - - -
625B GLY* 1.3 69.9 - - - -
627B THR* 1.3 79.6 + - - -
628B SER 2.8 4.5 + - - -
691B THR* 3.5 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