Contacts of the strand formed by residues 628 - 632 (chain A) in PDB entry 4N2F
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 628 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330A LYS* 2.6 33.4 + - - +
596A LYS* 2.9 44.3 + - + +
597A ASP* 3.5 13.2 - - - +
598A LEU* 2.9 29.2 + - - +
623A GLU* 5.3 1.1 - - - -
626A GLY 4.2 8.2 - - - +
627A LEU* 1.3 76.0 - - - +
629A CYS* 1.3 62.2 + - - +
630A THR* 3.9 1.9 + - - -
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Residues in contact with CYS 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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598A LEU* 3.8 7.6 - - - -
600A ILE* 3.8 26.5 - - + -
618A VAL* 4.9 1.3 - - - -
619A ARG* 2.9 53.9 + - + +
622A LEU* 4.0 29.2 - - - -
623A GLU* 4.5 9.9 + - - -
627A LEU 3.9 6.5 + - - -
628A GLU* 1.3 74.4 - - - +
630A THR* 1.3 61.9 + - - +
631A PHE* 4.1 5.4 - - + -
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Residues in contact with THR 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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323A GLU* 4.7 5.2 - - + +
326A ASN* 6.1 1.8 - - + -
327A LEU* 4.0 26.8 - - + +
330A LYS* 4.2 16.3 - - - -
598A LEU 2.9 12.8 + - - +
599A GLY* 3.4 2.6 - - - -
600A ILE* 2.8 25.7 + - - -
619A ARG* 4.8 1.6 - - - +
628A GLU 4.8 1.6 + - - -
629A CYS* 1.3 76.8 + - - +
631A PHE* 1.3 67.4 + - - +
632A ILE* 3.7 21.3 + - + +
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Residues in contact with PHE 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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323A GLU* 3.7 12.5 - - - +
588A MET* 4.2 13.5 - - - -
600A ILE* 3.2 40.8 - - + +
601A PRO 3.8 9.4 - - - -
602A LYS* 4.3 15.2 + - - +
603A PRO* 3.9 2.0 - - + -
615A GLU* 3.7 65.5 - - + +
618A VAL* 4.2 14.6 - - + -
619A ARG* 3.7 38.4 - - + +
629A CYS* 4.5 4.5 - - + -
630A THR* 1.3 77.4 - - - +
632A ILE* 1.3 62.3 + - - +
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Residues in contact with ILE 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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320A PHE* 3.7 31.2 - - + +
323A GLU* 3.5 38.4 - - + +
324A VAL* 3.9 15.9 - - + +
327A LEU* 4.6 8.3 - - + -
592A ILE* 5.2 1.6 - - + -
599A GLY* 4.0 15.3 - - - -
600A ILE 2.8 12.8 + - - +
601A PRO* 3.6 4.7 - - - +
602A LYS* 3.0 20.0 + - - +
630A THR* 3.7 29.2 - - + +
631A PHE* 1.3 72.8 - - - +
633A ASP* 1.3 60.4 + - - +
634A ASP* 3.3 8.4 + - - +
706A MPD 4.4 11.7 - - + +
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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