Contacts of the strand formed by residues 645 - 652 (chain A) in PDB entry 5L6P
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 645 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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641A ALA* 3.8 5.2 - - - +
642A GLY* 2.8 35.5 + - - +
643A GLU 3.7 0.4 - - - -
644A PHE* 1.3 79.6 - - - +
646A GLU* 1.3 61.2 + - - -
666A THR 3.3 8.7 + - - -
668A LYS* 4.1 13.9 - - - -
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Residues in contact with GLU 646 (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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638A VAL* 4.7 22.3 - - + +
640A GLY 4.0 9.6 - - - +
641A ALA* 4.4 2.9 - - + +
642A GLY 4.3 0.2 - - - +
645A GLY* 1.3 75.8 - - - +
647A VAL* 1.3 65.1 + - - +
648A CYS* 5.0 4.9 - - - -
664A ILE 4.5 0.2 - - - -
665A LYS* 3.5 4.5 - - - +
666A THR* 2.9 46.9 + - - +
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Residues in contact with VAL 647 (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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638A VAL* 3.9 1.6 - - - +
639A ILE* 3.2 16.1 + - + -
640A GLY 3.0 30.5 + - - +
642A GLY* 3.7 22.4 - - - +
646A GLU* 1.3 77.9 - - - +
648A CYS* 1.3 64.1 + - - +
663A ALA* 5.3 2.2 - - + -
664A ILE 3.5 8.3 - - - +
665A LYS* 4.0 14.4 - - + -
778A GLY 4.6 7.2 - - - +
779A LEU* 3.4 34.3 - - + +
1001A 6P8 4.3 26.0 - - + +
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Residues in contact with CYS 648 (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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635A ILE* 3.8 37.7 - - + -
637A GLU 3.4 13.2 - - - +
638A VAL* 3.7 16.4 - - + -
639A ILE* 3.8 7.9 - - - -
646A GLU* 5.0 2.7 - - - -
647A VAL* 1.3 79.1 - - - +
649A ARG* 1.3 62.8 + - - +
663A ALA* 3.5 3.1 - - - +
664A ILE* 2.8 58.7 + - - +
666A THR* 4.6 11.9 - - - -
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Residues in contact with ARG 649 (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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635A ILE* 3.9 3.1 - - - +
636A GLU* 2.8 50.3 + - - +
637A GLU* 2.8 27.4 + - - +
639A ILE* 4.0 13.7 - - + +
648A CYS* 1.3 73.2 - - - +
650A GLY* 1.3 58.1 + - - +
661A PHE* 3.6 33.7 - - + -
662A VAL 3.6 4.9 - - - +
664A ILE* 4.7 1.1 - - - -
713A PHE* 3.6 49.8 - - + -
715A GLU* 6.0 3.0 - - - +
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Residues in contact with GLY 650 (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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634A LYS 3.3 13.2 - - - -
636A GLU* 3.8 9.6 - - - -
648A CYS 4.0 0.4 + - - -
649A ARG* 1.3 75.7 - - - +
651A ARG* 1.3 59.7 + - - -
661A PHE* 3.5 16.7 - - - -
662A VAL* 2.8 33.2 + - - -
664A ILE* 3.8 11.4 - - - +
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Residues in contact with ARG 651 (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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632A CYS 3.7 0.9 - - - +
633A VAL* 3.5 7.3 - - - +
634A LYS* 2.9 36.9 + - + +
636A GLU* 5.4 2.0 - - + +
650A GLY* 1.3 73.7 - - - +
652A LEU* 1.3 60.4 + - - +
659A GLU* 3.5 30.3 - - - +
660A VAL 3.5 9.0 - - - +
661A PHE* 5.3 7.2 - - + -
662A VAL* 3.9 3.5 - - - +
664A ILE* 4.6 0.4 - - - +
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Residues in contact with LEU 652 (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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632A CYS* 3.5 13.7 - - + +
633A VAL* 3.7 19.5 - - + -
651A ARG* 1.3 73.8 - - - +
653A LYS* 1.3 65.4 + - - +
654A GLN* 3.8 16.9 + - + +
658A ARG 4.3 0.5 - - - +
659A GLU* 3.4 8.6 - - - +
660A VAL* 3.1 37.1 + - + +
662A VAL* 3.8 26.0 - - + +
698A GLU* 4.1 34.5 - - + +
710A LEU* 4.6 11.0 - - + -
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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