Contacts of the helix formed by residues 613 - 623 (chain B) in PDB entry 1MS4
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 ASN 613 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610B ARG* 4.7 1.8 - - - +
611B GLN 3.7 1.9 + - - +
612B LEU* 1.3 75.9 - - - +
614B ALA* 1.3 64.2 + - - +
615B GLU* 3.1 10.4 + - - +
616B GLU* 2.8 49.0 + - - +
617B ILE* 3.1 24.8 + - - +
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Residues in contact with ALA 614 (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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559B TYR* 5.9 3.6 - - + -
613B ASN* 1.3 75.4 - - - +
615B GLU* 1.3 58.9 + - - +
617B ILE* 3.5 8.6 + - - +
618B ARG* 3.0 27.9 + - - +
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Residues in contact with GLU 615 (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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412B PRO* 3.8 37.0 - - + +
613B ASN* 3.1 10.0 + - - +
614B ALA* 1.3 76.0 - - - +
616B GLU* 1.3 61.1 + - + +
618B ARG* 3.1 6.9 + - - +
619B THR* 2.7 41.5 + - - +
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Residues in contact with GLU 616 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B THR* 3.8 27.1 + - + +
610B ARG* 2.9 39.9 + - - -
612B LEU* 3.5 8.9 - - + -
613B ASN* 2.8 49.1 + - - +
615B GLU* 1.3 78.7 - - + +
617B ILE* 1.3 58.4 + - - +
619B THR* 3.2 8.6 + - - -
620B LEU* 2.9 34.9 + - - +
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Residues in contact with ILE 617 (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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546B HIS* 4.4 1.5 + - - +
548B VAL* 4.3 24.5 - - + -
550B THR* 4.3 8.3 - - + -
559B TYR* 3.8 46.7 - - + +
562B GLY* 4.1 23.3 - - - +
612B LEU* 3.8 28.0 - - + +
613B ASN 3.1 23.6 + - - +
614B ALA* 3.7 6.7 - - - +
616B GLU* 1.3 75.1 - - - +
618B ARG* 1.3 65.5 + - - +
620B LEU* 2.9 19.9 + - - +
621B PHE* 3.1 11.1 + - - +
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Residues in contact with ARG 618 (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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561B ASP 5.8 0.2 - - - -
562B GLY* 5.1 8.5 - - - +
563B GLU* 5.2 9.4 - - - -
614B ALA 3.0 17.8 + - - +
615B GLU* 3.6 5.8 - - - +
617B ILE* 1.3 78.1 - - - +
619B THR* 1.3 63.7 + - - +
621B PHE* 3.3 20.6 + - - +
622B LEU* 3.1 56.9 + - + +
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Residues in contact with THR 619 (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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397B THR* 3.8 19.5 - - + +
412B PRO* 3.1 48.6 - - + +
413B ALA 3.9 11.4 + - - +
414B VAL* 4.0 8.7 - - + +
615B GLU* 2.7 24.9 + - - +
616B GLU* 3.5 8.4 - - - -
618B ARG* 1.3 74.9 - - - +
620B LEU* 1.3 61.4 + - - +
622B LEU* 3.5 8.1 + - - +
623B SER* 2.8 26.4 + - - -
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Residues in contact with LEU 620 (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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414B VAL* 4.1 27.4 - - + -
415B THR* 5.5 2.9 - - + +
485B VAL* 4.3 13.2 - - + -
546B HIS* 3.7 21.3 - - + +
548B VAL* 5.9 0.9 - - + -
606B LEU* 3.8 22.2 - - + -
608B TYR* 4.0 16.6 - - + +
612B LEU* 3.6 30.7 - - + -
616B GLU 2.9 12.9 + - - +
617B ILE* 2.9 10.7 + - - +
619B THR* 1.3 79.2 - - - +
621B PHE* 1.3 61.3 + - - +
623B SER* 3.1 16.7 + - - +
624B GLN* 3.2 11.1 + - - -
627B ILE* 4.8 9.5 - - + +
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Residues in contact with PHE 621 (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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546B HIS* 3.5 30.4 + - + -
561B ASP* 3.2 57.0 - - + -
562B GLY* 4.1 8.5 - - - +
617B ILE 3.1 8.7 + - - +
618B ARG* 3.3 18.6 + - - +
620B LEU* 1.3 77.2 - - - +
622B LEU* 1.3 87.7 + - + +
623B SER 3.2 0.7 + - - -
624B GLN* 3.4 23.8 + - - +
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Residues in contact with LEU 622 (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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397B THR* 5.8 0.7 - - - -
398B PRO* 3.5 50.1 - - + +
399B ALA 5.5 0.7 - - - +
618B ARG* 3.1 55.3 + - + +
619B THR* 4.0 6.5 - - - +
621B PHE* 1.3 100.8 - - + +
623B SER* 1.3 59.8 + - - +
624B GLN 3.7 0.3 + - - -
625B ASP* 5.2 2.3 + - - +
626B LEU* 4.8 1.4 - - - +
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Residues in contact with SER 623 (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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395B ILE* 5.0 0.4 - - - -
397B THR* 4.1 23.3 - - - -
414B VAL* 3.5 19.8 - - - +
619B THR 2.8 21.7 + - - -
620B LEU* 3.1 8.8 + - - -
622B LEU* 1.3 77.6 - - - +
624B GLN* 1.3 64.1 + - - +
625B ASP 3.3 2.7 - - - -
626B LEU* 2.8 30.4 + - - -
627B ILE* 3.5 15.9 + - - +
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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