Contacts of the strand formed by residues 487 - 495 (chain A) in PDB entry 4WPN
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 THR 487 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A ILE* 4.1 15.7 - - + -
157A HIS* 4.1 31.5 + - + +
158A GLU 3.1 12.8 - - - +
160A ILE* 3.6 12.2 - - - +
186A CYS* 3.9 16.4 - - + +
483A PHE 3.7 11.4 - - - +
484A HIS* 3.2 25.6 + - - +
485A GLU 4.6 0.5 - - - -
486A TYR* 1.3 84.1 - - - +
488A GLU* 1.3 61.0 + - - +
489A VAL* 4.2 6.7 + - - +
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Residues in contact with GLU 488 (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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156A ARG 3.6 0.9 - - - +
158A GLU* 2.7 38.5 + - + +
159A PRO 4.3 3.4 - - - +
160A ILE* 3.8 30.4 - - - +
265A ARG* 2.9 44.4 + - - +
487A THR* 1.3 75.8 - - - +
489A VAL* 1.3 70.8 + - - +
490A LYS* 3.6 0.9 + - - +
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Residues in contact with VAL 489 (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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155A THR* 4.1 28.9 - - + -
156A ARG 3.5 4.5 - - - +
157A HIS* 4.0 28.0 - - + +
487A THR* 4.8 7.0 - - - +
488A GLU* 1.3 83.9 + - - +
490A LYS* 1.3 62.6 + - - +
491A THR* 4.2 4.9 + - - +
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Residues in contact with LYS 490 (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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154A TYR 3.9 0.2 - - - +
155A THR* 3.1 5.3 - - - -
156A ARG* 2.8 50.6 + - + +
158A GLU* 2.7 39.1 + - - +
488A GLU 3.6 0.6 + - - -
489A VAL* 1.3 76.0 - - - +
491A THR* 1.3 70.9 + - - +
492A VAL* 3.9 18.2 + - + +
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Residues in contact with THR 491 (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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145A ILE* 5.7 1.3 - - + -
153A THR* 3.8 26.7 - - + -
154A TYR 3.6 3.8 - - - +
155A THR* 3.9 13.9 - - + +
489A VAL* 4.2 5.2 + - - +
490A LYS* 1.3 78.2 - - - +
492A VAL* 1.3 65.7 + - - +
493A THR* 3.8 10.1 + - - +
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Residues in contact with VAL 492 (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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152A PHE 3.6 1.7 - - - +
153A THR* 3.2 3.8 - - - +
154A TYR* 2.8 84.6 + - + +
156A ARG* 4.6 5.6 - - - -
490A LYS* 4.1 23.6 - - + +
491A THR* 1.3 77.0 - - - +
493A THR* 1.3 63.9 + - - +
494A VAL* 4.2 12.6 - - + -
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Residues in contact with THR 493 (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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147A ILE* 4.0 11.5 - - + +
151A PHE* 3.9 28.7 - - + -
152A PHE 3.5 2.9 - - - -
153A THR* 2.9 29.1 + - - +
491A THR* 3.8 10.6 + - - +
492A VAL* 1.3 74.6 - - - +
494A VAL* 1.3 63.6 + - - +
495A LYS 4.2 0.9 + - - -
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Residues in contact with VAL 494 (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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151A PHE* 3.2 6.3 - - - -
152A PHE* 2.8 62.0 + - + +
154A TYR* 4.6 5.2 - - + -
492A VAL* 4.2 19.1 - - + -
493A THR* 1.3 75.5 - - - +
495A LYS* 1.3 73.3 + - - +
496A ILE* 3.4 8.0 + - + +
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Residues in contact with LYS 495 (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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150A ASN 4.5 1.1 - - - +
151A PHE* 3.7 25.3 - - + -
493A THR 4.2 1.4 + - - -
494A VAL* 1.3 80.2 - - - +
496A ILE* 1.3 77.3 + - - +
497A SER* 5.7 2.6 - - - +
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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