Contacts of the strand formed by residues 627 - 634 (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 GLU 627 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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623A LYS* 3.7 1.4 - - - +
624A LYS* 2.8 59.7 + - + +
625A GLY 3.4 1.0 + - - -
626A LYS* 1.3 82.4 - - - +
628A LEU* 1.3 63.3 + - - +
629A PHE* 3.7 1.2 + - - +
680A VAL* 3.1 28.9 - - + +
681A ILE 3.2 13.2 - - - +
682A ASN* 4.6 4.5 - - + +
683A LEU* 4.3 1.8 - - - +
1133A NAG 5.1 11.4 - - + +
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Residues in contact with LEU 628 (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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621A VAL* 3.9 22.7 - - + -
622A GLN 3.8 0.4 - - - -
623A LYS* 3.8 33.2 - - + -
627A GLU* 1.3 71.4 - - - +
629A PHE* 1.3 60.7 + - - +
630A ILE* 3.7 15.5 + - + +
658A TYR* 4.8 6.5 - - + -
680A VAL* 3.3 6.1 - - - -
681A ILE* 2.8 53.4 + - + -
683A LEU* 4.0 22.4 - - + +
690A VAL* 3.9 34.1 - - + -
692A VAL* 4.7 6.5 - - + -
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Residues in contact with PHE 629 (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 3.7 1.0 - - - +
621A VAL* 3.5 4.5 - - - -
622A GLN* 2.8 48.6 + - + +
624A LYS* 3.7 37.7 - - + +
627A GLU* 3.7 3.7 + - + +
628A LEU* 1.3 72.6 - - - +
630A ILE* 1.3 60.5 + - - +
631A GLN* 4.1 24.2 - - + -
678A SER* 4.1 25.6 - - - -
679A GLY 3.3 20.2 - - - -
680A VAL* 3.9 16.6 - - + +
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Residues in contact with ILE 630 (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* 3.8 12.3 - - + -
620A THR 3.4 1.1 - - - -
621A VAL* 3.6 32.3 - - + -
628A LEU* 3.8 20.6 - - + +
629A PHE* 1.3 84.8 - - - +
631A GLN* 1.3 65.6 + - - +
656A LEU* 3.6 28.5 - - + -
674A LEU* 3.6 15.5 - - + -
678A SER* 3.1 8.1 - - - -
679A GLY* 3.0 40.0 + - - +
681A ILE* 4.3 19.3 - - + -
692A VAL* 5.3 2.9 - - + -
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Residues in contact with GLN 631 (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 3.6 0.4 - - - +
619A VAL* 3.2 7.6 - - - +
620A THR* 2.7 53.0 + - - +
629A PHE* 4.1 22.7 - - + -
630A ILE* 1.3 79.4 - - - +
632A GLN* 1.3 60.8 + - - +
633A GLU* 5.7 2.7 - - - +
674A LEU* 4.4 4.7 - - - -
677A LYS* 3.1 31.5 - - - +
678A SER* 3.9 14.1 + - - +
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Residues in contact with GLN 632 (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* 4.2 5.8 - - + -
618A LEU 3.4 6.1 - - - +
619A VAL* 4.7 1.8 - - + -
631A GLN* 1.3 75.8 - - - +
633A GLU* 1.3 66.1 + - - +
650A TYR 4.7 0.2 - - - +
651A LEU* 3.6 17.9 - - + +
652A TRP* 2.8 61.3 + - - +
654A ILE* 3.6 24.5 - - + +
674A LEU* 3.8 11.8 + - + +
675A ASP 4.3 0.4 + - - -
676A LYS 3.0 29.7 + - - +
677A LYS* 3.1 29.0 + - - +
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Residues in contact with GLU 633 (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* 3.2 6.2 - - - +
618A LEU* 2.7 63.4 + - + +
620A THR* 4.8 6.6 + - - +
631A GLN* 5.7 2.8 - - - +
632A GLN* 1.3 78.3 - - - +
634A ARG* 1.3 65.8 + - - +
652A TRP* 4.3 5.6 - - - -
677A LYS* 5.3 7.1 + - - -
743A LYS* 4.1 14.4 + - - -
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Residues in contact with ARG 634 (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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523A SER 5.0 3.0 + - - -
524A LEU 5.3 2.0 + - - -
525A ASN* 4.9 8.5 + - - +
613A GLN* 5.0 4.0 - - - +
614A LYS* 3.8 41.0 + - - +
615A GLY* 5.6 3.2 - - - -
633A GLU* 1.3 86.4 - - - +
635A PHE* 1.3 64.1 + - - +
636A PHE* 3.3 72.8 + - + +
649A SER* 3.1 34.5 - - - +
650A TYR 5.3 0.2 - - - +
652A TRP* 4.0 23.5 - - + -
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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