Contacts of the strand formed by residues 619 - 625 (chain B) in PDB entry 1RL3
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 619 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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554B VAL 4.3 0.2 - - - +
555B SER* 3.5 6.3 + - - -
556B PHE* 3.0 39.2 + - + +
575B ILE* 4.9 0.4 - - + -
577B GLN 3.0 14.1 - - - +
578B GLY* 3.5 25.1 - - - -
579B GLU 3.5 10.1 - - - +
580B MET* 3.9 18.6 - - + -
615B ALA* 4.0 10.8 - - + -
617B THR 3.0 14.1 + - - +
618B ASN* 1.3 75.0 - - - +
620B LYS* 1.3 59.4 + - - +
621B LEU* 3.7 27.6 - - + -
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Residues in contact with LYS 620 (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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522B THR* 6.2 2.2 - - - +
525B ALA* 4.8 8.5 - - - +
553B PRO* 4.5 7.6 - - + +
554B VAL 3.5 14.1 - - - +
555B SER* 4.5 10.3 - - - +
576B ASP* 3.2 34.5 + - + +
577B GLN* 3.1 23.2 + - + +
619B VAL* 1.3 73.5 - - - +
621B LEU* 1.3 81.1 + - - +
622B TRP* 4.0 32.9 - - - -
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Residues in contact with LEU 621 (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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553B PRO* 3.6 5.0 - - - +
554B VAL* 2.6 47.6 + - + +
556B PHE* 4.4 3.4 - - + -
562B VAL* 4.3 11.9 - - + -
573B TYR* 3.6 27.6 - - + -
574B VAL 3.6 6.1 - - - +
575B ILE* 3.8 31.2 - - + +
580B MET* 4.2 10.8 - - + -
598B PHE* 3.9 17.7 - - + -
619B VAL* 3.7 29.4 - - + -
620B LYS* 1.3 85.9 - - - +
622B TRP* 1.3 67.1 + - - +
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Residues in contact with TRP 622 (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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518B LYS* 4.5 4.3 - - + -
522B THR* 3.5 25.1 - - + -
525B ALA* 3.7 14.8 - - + -
526B LEU* 3.6 44.2 - - + -
529B ALA* 3.8 16.4 - - + +
551B MET* 4.4 14.4 - - + +
552B PHE 3.9 6.5 - - - -
553B PRO* 3.7 42.6 - - + -
572B PHE 3.7 0.9 - - - +
573B TYR* 3.4 2.5 - - - -
574B VAL* 2.8 53.9 + - + +
576B ASP* 2.6 40.9 + - + -
620B LYS* 4.0 14.1 - - - -
621B LEU* 1.3 76.2 - - - +
623B GLY* 1.3 61.3 + - - +
624B ILE* 5.3 0.5 - - - +
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Residues in contact with GLY 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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551B MET* 3.4 4.2 - - - +
552B PHE* 3.1 52.0 + - - -
554B VAL* 4.5 0.8 - - - +
572B PHE 3.3 9.4 - - - -
573B TYR* 3.8 15.3 - - - -
621B LEU 4.0 1.0 - - - -
622B TRP* 1.3 75.2 - - - +
624B ILE* 1.3 64.3 + - - +
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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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547B ILE* 4.3 22.4 - - + -
550B ALA* 4.2 13.7 - - + +
551B MET* 4.1 25.8 - - + -
552B PHE* 3.2 11.2 - - - -
571B ASN* 2.6 38.2 - - - +
572B PHE* 3.1 43.7 + - + +
574B VAL* 6.5 0.2 - - + -
622B TRP 5.3 0.4 - - - +
623B GLY* 1.3 74.8 - - - +
625B ASP* 1.3 67.9 + - - +
628B SER* 4.0 18.8 - - - -
629B TYR* 4.5 11.2 - - + +
633B LEU* 5.1 7.0 - - + -
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Residues in contact with ASP 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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511B TYR* 5.3 2.3 + - - -
514B LYS* 3.3 39.5 - - + +
550B ALA* 4.2 6.1 + - - +
552B PHE* 4.3 3.3 - - + -
570B ASP 4.9 0.2 - - - +
571B ASN* 3.3 11.7 - - - +
624B ILE* 1.3 73.7 - - - +
626B ARG* 1.3 61.2 + - + +
627B ASP* 3.3 20.7 - - - +
628B SER* 2.7 45.0 + - - -
629B TYR* 2.8 24.2 + - - +
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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
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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