Contacts of the strand formed by residues 649 - 653 (chain A) in PDB entry 3RA4
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 ILE 649 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A TYR* 3.2 5.8 - - - +
285A PHE* 3.0 48.6 + - + +
287A PHE* 4.2 14.4 - - + -
316A PHE* 3.6 44.0 - - + -
345A VAL* 4.0 20.6 - - + -
346A PHE 3.7 4.9 - - - +
347A THR* 4.2 3.6 - - + -
412A PHE* 4.4 4.7 - - + -
414A PHE* 3.5 32.5 - - + -
647A PRO 3.6 10.3 + - - +
648A GLN* 1.3 74.8 - - - +
650A LEU* 1.3 62.6 + - - +
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Residues in contact with LEU 650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A TRP* 3.8 17.1 - - + -
283A GLY 3.4 10.5 - - - +
284A TYR* 4.4 4.9 - - + -
344A GLN 3.8 0.2 - - - +
345A VAL* 3.3 7.6 - - - +
346A PHE* 3.0 65.5 + - + +
348A ASP* 4.5 1.6 - - + -
353A LEU* 3.6 13.2 - - + -
378A TYR* 3.8 32.1 - - + -
398A LEU* 3.4 20.0 - - + -
648A GLN* 4.1 22.2 - - + +
649A ILE* 1.3 76.7 - - - +
651A ILE* 1.3 62.0 + - - +
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Residues in contact with ILE 651 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A TRP* 4.0 19.7 - - + -
250A LEU* 3.7 21.2 - - + +
282A TRP* 3.5 2.1 - - - -
283A GLY* 2.7 49.2 + - - -
284A TYR 4.1 2.7 - - - +
285A PHE* 3.7 35.4 - - + -
318A LEU* 4.1 7.2 - - + -
343A ILE* 3.9 24.5 - - + -
344A GLN 3.1 11.4 - - - +
345A VAL* 4.0 7.0 - - + -
375A ILE* 4.2 9.2 - - + -
650A LEU* 1.3 75.8 - - - +
652A LYS* 1.3 66.2 + - - +
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Residues in contact with LYS 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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250A LEU* 4.0 6.5 - - - -
256A HIS* 5.9 3.4 + - - +
281A PRO* 3.5 32.6 - - + +
282A TRP* 3.4 32.3 - - + +
343A ILE* 3.2 4.0 - - - +
344A GLN* 2.7 61.7 + - + +
399A GLU* 2.5 36.4 + - - +
651A ILE* 1.3 78.1 - - - +
653A ASN* 1.3 79.2 + - - +
654A THR 3.7 0.3 + - - -
655A PRO* 4.1 17.1 - - + +
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Residues in contact with ASN 653 (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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250A LEU* 3.1 32.4 - - - +
251A PRO 3.5 11.3 + - - +
252A THR* 4.6 11.4 - - - +
256A HIS* 4.4 8.8 + - + -
323A VAL* 5.3 3.5 - - + +
342A THR 4.1 3.8 - - - +
343A ILE* 3.5 12.3 - - - +
652A LYS* 1.3 86.6 - - - +
654A THR* 1.3 67.3 + - - +
655A PRO* 3.4 6.1 - - - +
675A GLN* 4.0 11.1 - - + +
676A TYR* 3.7 8.7 - - - -
677A SER* 2.6 37.8 + - - -
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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