Contacts of the strand formed by residues 674 - 680 (chain A) in PDB entry 2HWK
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 TYR 674 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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633A THR* 3.5 13.0 - - - +
634A VAL 3.7 13.2 - - - -
635A LEU* 3.5 46.4 - - + -
647A MET 5.5 0.4 - - - -
649A ASP* 2.4 41.1 + - + +
659A PHE* 3.3 12.0 - - - -
671A VAL* 4.7 0.4 - - + -
672A PRO* 3.3 45.7 - - + +
673A LYS* 1.3 79.1 - - - +
675A ASP* 1.3 61.8 + - - +
676A ILE 3.5 16.8 - - - +
677A ILE* 3.9 5.6 - - + -
710A HIS 2.8 12.3 + - - +
711A LEU* 3.4 7.3 - - - +
712A ASN* 2.8 28.3 + - - +
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Residues in contact with ASP 675 (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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630A LYS 4.8 1.4 - - - +
631A GLY* 3.8 17.9 - - - -
632A ARG* 2.7 34.9 + - - +
633A THR* 3.1 18.2 + - - +
674A TYR* 1.3 74.2 - - - +
676A ILE* 1.3 59.2 + - - +
711A LEU* 4.6 0.7 - - - -
712A ASN* 2.7 30.8 + - - +
715A GLY* 3.2 9.6 - - - -
716A THR* 2.7 30.5 + - - -
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Residues in contact with ILE 676 (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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626A VAL* 4.5 5.8 - - + +
629A LEU* 3.6 42.6 - - + +
630A LYS 3.3 30.3 - - - +
631A GLY* 3.8 8.3 - - - -
633A THR 3.1 7.8 + - - +
634A VAL* 3.3 28.4 - - + -
635A LEU 2.9 23.4 + - - -
646A LYS* 4.2 4.7 - - - -
674A TYR* 3.5 2.3 - - - +
675A ASP* 1.3 86.5 - - + +
677A ILE* 1.3 77.6 + - - +
678A PHE* 4.6 2.0 - - + +
716A THR* 3.3 15.7 - - + +
718A VAL* 5.4 0.4 - - + -
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Residues in contact with ILE 677 (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 LEU* 3.3 24.5 - - + +
637A VAL* 4.1 19.7 - - + -
667A ILE* 5.2 0.9 - - + -
674A TYR* 3.9 8.1 - - + -
676A ILE* 1.3 81.7 - - - +
678A PHE* 1.3 61.8 + - - +
679A VAL* 4.1 4.9 - - + -
707A ALA* 3.5 41.7 - - + +
710A HIS* 3.4 33.9 - - + +
711A LEU* 3.6 13.7 - - + -
716A THR 3.0 7.9 + - - +
717A CYS* 3.6 3.2 - - - -
718A VAL* 2.8 33.6 + - - +
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Residues in contact with PHE 678 (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 PHE* 3.7 29.6 - + + -
626A VAL* 4.0 23.3 - - + -
634A VAL* 5.0 1.8 - - + +
635A LEU 2.8 12.1 + - - +
636A VAL* 3.4 10.3 - - + -
637A VAL* 2.7 33.1 + - - +
641A LEU* 3.5 29.2 - - + -
676A ILE* 4.2 2.2 - - + +
677A ILE* 1.3 73.9 - - - +
679A VAL* 1.3 61.7 + - - +
680A ASN* 3.2 47.1 + - + -
718A VAL* 3.4 40.6 - - + -
720A ILE* 4.1 4.9 - - + -
758A LEU* 4.0 12.3 - - + -
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Residues in contact with VAL 679 (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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637A VAL* 3.8 9.9 - - + +
677A ILE* 4.4 14.4 - - + -
678A PHE* 1.3 75.2 - - - +
680A ASN* 1.3 57.9 + - - +
681A VAL* 3.1 30.0 + - + +
696A HIS* 6.1 2.7 - - + +
699A LYS* 5.4 1.8 - - + +
703A LEU* 4.1 19.1 - - + +
704A THR* 3.8 36.1 - - + +
707A ALA* 5.0 0.2 - - + -
717A CYS* 4.7 3.4 - - - -
718A VAL 2.7 16.0 + - - +
719A SER* 3.7 13.8 - - - +
720A ILE* 3.2 23.6 + - - +
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Residues in contact with ASN 680 (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 GLN* 6.0 0.8 - - - +
622A PHE* 4.4 0.9 - - - -
636A VAL* 4.2 3.1 - - + -
637A VAL 2.7 17.2 + - - +
639A GLU* 2.8 68.7 + - - +
640A LYS 3.7 9.1 + - - -
641A LEU* 4.1 12.4 - - - +
678A PHE* 3.2 33.2 + - + -
679A VAL* 1.3 69.3 - - - +
681A VAL* 1.3 55.7 + - - +
682A ARG* 3.4 24.7 + - - +
720A ILE* 3.6 6.8 - - - +
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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