Contacts of the strand formed by residues 617 - 624 (chain A) in PDB entry 5MJ6
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 PRO 617 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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610A TRP* 3.5 23.1 - - + -
616A PHE* 1.4 94.8 - - + +
618A LEU* 1.3 60.7 + - - +
619A VAL* 4.7 0.7 - - + -
632A GLN* 4.2 9.6 - - + -
633A GLU 3.2 10.3 - - - +
652A TRP* 3.5 26.7 - - + -
654A ILE* 3.7 30.3 - - + -
699A TYR 4.0 1.3 - - - +
700A TYR* 3.3 32.2 - - + +
701A ILE 3.4 6.9 + - - -
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Residues in contact with LEU 618 (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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616A PHE 3.8 1.8 + - - -
617A PRO* 1.3 71.1 - - - +
619A VAL* 1.3 60.2 - - - +
620A THR* 3.7 13.5 + - - +
631A GLN 3.6 0.5 - - - +
632A GLN* 3.4 3.3 - - - -
633A GLU* 2.7 59.7 + - + +
634A ARG 5.4 0.4 - - - +
635A PHE* 3.8 27.6 - - + +
701A ILE* 3.7 22.0 - - + +
703A HIS* 3.8 23.6 - - + +
738A LEU* 3.8 16.6 - - + -
741A LEU* 4.8 2.2 - - + -
743A LYS* 3.6 27.6 - - + -
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Residues in contact with VAL 619 (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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617A PRO* 4.7 0.9 - - + -
618A LEU* 1.3 72.6 - - - +
620A THR* 1.3 61.1 + - - +
621A VAL* 4.2 13.2 - - + -
630A ILE* 3.8 22.7 - - + -
631A GLN 3.2 10.8 - - - +
632A GLN* 4.7 1.1 - - + -
654A ILE* 4.1 22.2 - - + -
656A LEU* 4.0 18.8 - - + -
674A LEU* 5.4 0.7 - - + -
692A VAL* 5.1 0.9 - - + -
700A TYR* 3.6 30.7 - - + -
701A ILE 2.9 13.5 + - - +
702A VAL* 3.2 12.2 - - + +
703A HIS 2.9 24.5 + - - -
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Residues in contact with THR 620 (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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618A LEU* 3.7 18.7 + - - +
619A VAL* 1.3 74.4 - - - +
621A VAL* 1.3 69.3 + - - +
622A GLN* 5.9 1.6 - - + -
629A PHE 3.7 0.9 - - - +
630A ILE* 3.4 6.4 - - - +
631A GLN* 2.7 52.7 + - + +
633A GLU* 4.8 7.1 + - - -
703A HIS* 3.3 26.9 - - + +
704A TYR 5.4 0.2 - - - -
705A ALA* 5.4 2.9 - - - +
743A LYS* 5.8 0.7 - - - -
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Residues in contact with VAL 621 (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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619A VAL* 4.2 7.6 - - + -
620A THR* 1.3 79.3 - - - +
622A GLN* 1.3 65.9 + - - +
623A LYS 4.9 0.4 - - - +
628A LEU* 3.9 26.5 - - + -
629A PHE 3.5 2.9 - - - -
630A ILE* 3.6 25.1 - - + -
690A VAL* 5.1 2.9 - - + -
692A VAL* 3.8 16.8 - - + -
702A VAL* 3.7 24.0 - - + -
703A HIS 2.8 8.5 + - - +
704A TYR* 3.4 21.0 - - + +
705A ALA 2.9 25.8 + - - -
708A ASP* 4.4 2.2 - - - +
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Residues in contact with GLN 622 (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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620A THR* 5.9 2.5 - - + -
621A VAL* 1.3 78.1 - - - +
623A LYS* 1.3 67.0 + - - +
624A LYS* 3.1 38.3 + - + +
628A LEU* 4.4 2.7 - - - -
629A PHE* 2.8 46.1 + - + +
705A ALA* 4.0 20.8 - - + +
708A ASP* 3.8 4.5 - - - +
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Residues in contact with LYS 623 (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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622A GLN* 1.3 75.4 - - - +
624A LYS* 1.3 60.5 + - - +
625A GLY* 3.6 26.3 + - - +
627A GLU 4.3 2.2 - - - +
628A LEU* 3.8 21.9 - - + +
683A LEU* 4.4 4.0 - - + -
686A GLU* 5.2 5.3 + - - -
687A VAL* 3.1 47.2 + - + +
688A LEU 4.0 10.7 + - - -
689A TRP* 5.5 0.8 - - - +
690A VAL* 4.9 2.7 - - + -
708A ASP* 3.0 32.8 + - - +
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Residues in contact with LYS 624 (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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622A GLN* 3.1 37.3 + - + +
623A LYS* 1.3 74.4 - - - +
625A GLY* 1.3 61.4 + - - +
626A LYS 3.2 0.3 + - - -
627A GLU* 2.8 46.4 + - + +
629A PHE* 3.7 34.7 - - + -
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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