Contacts of the helix formed by residues 628 - 635 (chain B) in PDB entry 3RFU
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 ASP 628 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426B ASP* 3.5 20.3 - - - +
602B PRO* 3.7 11.5 - - - +
605B LYS* 3.2 37.1 - - + +
621B MET* 3.4 14.6 - - + -
624B ASP 3.2 19.1 + - - +
625B GLY 3.7 1.2 - - - +
627B ASN* 1.3 100.1 + - - +
629B ALA* 1.3 57.4 + - - +
630B PRO* 3.4 4.3 - - - -
631B ALA* 3.0 8.4 + - - +
632B LEU* 2.8 44.7 + - - +
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Residues in contact with ALA 629 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B LEU* 5.8 1.1 - - + -
318B ILE* 5.3 2.9 - - + -
322B VAL* 5.1 7.2 - - + -
625B GLY 4.6 0.9 - - - +
626B VAL 3.0 19.7 - - - +
627B ASN 2.6 8.7 + - - +
628B ASP* 1.3 70.4 - - - +
630B PRO* 1.3 66.6 - - + +
631B ALA 2.9 1.3 - - - -
632B LEU* 2.8 29.8 + - - +
633B ALA* 3.0 14.4 + - - +
647B VAL* 3.5 24.9 - - + -
648B ALA 4.9 0.4 - - - +
651B SER* 4.0 11.8 - - - +
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Residues in contact with PRO 630 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B ILE* 4.3 15.3 - - + +
321B MET* 3.9 35.2 - - + -
322B VAL* 4.5 16.6 - - + +
325B ALA* 4.4 2.3 - - - +
602B PRO* 3.3 28.7 - - + +
606B SER* 3.6 16.5 + - - +
626B VAL 4.3 0.4 - - - +
628B ASP* 3.5 3.8 - - - +
629B ALA* 1.3 95.9 - - + +
631B ALA* 1.3 55.3 + - - +
633B ALA 4.7 0.2 - - - +
634B LYS* 2.9 32.7 + - - +
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Residues in contact with ALA 631 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576B LEU* 6.0 0.2 - - + -
605B LYS* 4.0 17.0 - - + -
606B SER* 4.0 9.6 - - - +
609B VAL* 4.0 19.6 - - + +
621B MET* 3.7 24.9 - - + +
628B ASP 3.0 15.8 + - - +
629B ALA 2.9 0.4 - - - -
630B PRO* 1.3 81.3 - - - +
632B LEU* 1.3 62.5 + - - +
634B LYS* 4.0 1.5 - - - +
635B ALA* 3.1 26.0 + - - +
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Residues in contact with LEU 632 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621B MET* 3.2 33.9 - - + +
623B GLY* 4.7 6.1 - - - +
628B ASP* 2.8 50.2 + - - +
629B ALA* 2.8 12.2 + - - +
631B ALA* 1.3 81.0 - - - +
633B ALA* 1.3 63.0 + - - +
634B LYS 3.2 0.2 + - - -
635B ALA* 3.4 14.9 + - - +
638B GLY* 3.8 14.0 + - - -
639B ILE 3.8 21.3 - - - +
640B ALA* 4.9 1.1 - - - -
648B ALA* 4.4 21.5 - - + +
651B SER* 3.8 17.4 - - - +
652B ALA* 3.9 8.1 - - + -
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Residues in contact with ALA 633 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B ILE* 5.2 0.4 - - + -
322B VAL* 4.3 11.7 - - + +
325B ALA* 3.7 29.1 - - + +
326B GLN* 4.2 21.8 - - + -
329B ARG* 5.2 6.1 - - - +
629B ALA 3.0 9.9 + - - +
630B PRO 4.5 0.7 - - - +
632B LEU* 1.3 79.4 - - - +
634B LYS* 1.3 62.6 + - - +
635B ALA 3.8 4.4 - - - +
651B SER* 4.0 18.1 + - - +
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Residues in contact with LYS 634 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325B ALA* 3.7 18.7 - - + +
328B SER* 5.0 9.1 + - - -
606B SER* 3.9 24.7 - - - +
609B VAL* 4.3 10.1 - - + -
610B SER* 3.4 30.8 + - - +
613B LYS* 3.8 30.1 - - + +
630B PRO 2.9 22.5 + - - +
631B ALA* 4.0 4.0 - - - +
632B LEU 3.2 0.2 - - - -
633B ALA* 1.3 77.6 - - - +
635B ALA* 1.3 68.7 + - - +
636B ASP* 4.6 0.2 - - - -
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Residues in contact with ALA 635 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609B VAL* 3.8 19.2 - - + +
613B LYS* 4.2 2.2 - - - -
619B VAL 3.5 15.9 - - - +
621B MET* 3.8 11.4 - - + -
631B ALA 3.1 19.3 + - - +
632B LEU 3.4 9.7 + - - +
633B ALA 3.8 4.2 - - - +
634B LYS* 1.3 83.3 - - - +
636B ASP* 1.3 67.0 + - - +
637B ILE* 3.1 14.4 + - - +
638B GLY 4.8 0.2 + - - -
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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