Contacts of the helix formed by residues 615 - 626 (chain F) in PDB entry 6X34
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 CYS 615 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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613F ALA 4.7 0.9 - - - -
614F VAL* 1.3 78.7 - - - +
616F SER* 1.3 61.3 + - - +
617F ASN 3.5 1.1 - - - -
618F GLN* 4.0 5.2 - - - +
619F ASP* 3.1 35.8 + - - +
1678F ASN* 4.2 18.6 - - - +
2169F VAL* 4.5 20.6 - - - -
2170F GLN* 5.1 2.2 + - - -
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Residues in contact with SER 616 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578F ILE* 5.9 2.6 - - - +
614F VAL* 4.7 6.4 - - - +
615F CYS* 1.3 76.0 + - - +
617F ASN* 1.3 62.2 + - - +
619F ASP* 3.3 4.5 + - - +
620F LEU* 2.9 40.7 + - - +
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Residues in contact with ASN 617 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578F ILE* 4.0 27.4 - - + -
583F ILE* 4.4 4.4 - - + +
606F LEU* 4.0 17.5 - - + +
607F CYS* 5.0 2.5 - - - +
614F VAL* 3.9 20.2 - - + +
615F CYS 3.5 0.2 - - - -
616F SER* 1.3 80.6 + - - +
618F GLN* 1.3 59.2 + - - +
620F LEU* 3.3 9.3 + - - +
621F ILE* 2.9 30.0 + - - +
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Residues in contact with GLN 618 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607F CYS* 3.4 41.2 + - - +
608F VAL* 5.3 2.6 - - - +
613F ALA* 4.6 13.3 - - - +
614F VAL 3.4 20.6 + - - +
615F CYS 3.7 3.7 + - - +
616F SER 3.3 0.6 - - - -
617F ASN* 1.3 76.0 - - - +
619F ASP* 1.3 59.9 + - - +
621F ILE* 3.3 6.3 + - - +
622F THR* 2.7 34.8 + - - +
1672F ALA 4.5 3.0 + - - -
1673F VAL* 2.9 30.5 + - + +
1675F ALA 4.8 6.1 + - - -
1678F ASN* 2.4 37.6 + - - +
1681F VAL* 4.3 4.1 - - + +
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Residues in contact with ASP 619 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88E PRO* 5.6 10.5 - - - +
615F CYS* 3.1 24.0 + - - +
616F SER* 3.8 4.9 - - - +
618F GLN* 1.3 77.5 - - - +
620F LEU* 1.3 59.4 + - + +
622F THR* 3.3 7.7 + - - -
623F GLU* 2.9 31.2 + - - +
1678F ASN* 5.8 0.7 + - - +
1680F ARG* 3.9 36.0 + - - +
1681F VAL* 5.6 4.9 - - - +
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Residues in contact with LEU 620 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578F ILE* 6.3 3.1 - - + -
579F GLN* 4.2 5.6 - - - +
580F GLU* 3.8 39.0 - - + +
583F ILE* 3.7 19.3 - - + -
616F SER* 2.9 27.1 + - - +
617F ASN* 3.7 7.2 - - - +
618F GLN 3.3 0.2 - - - -
619F ASP* 1.3 77.8 - - + +
621F ILE* 1.3 57.4 + - - +
623F GLU* 3.3 4.3 + - + -
624F ASN* 2.9 45.4 + - - +
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Residues in contact with ILE 621 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583F ILE* 3.5 16.7 - - + +
587F ILE* 6.4 0.9 - - - -
603F LEU* 4.9 12.3 - - + -
617F ASN 2.9 17.4 + - - +
618F GLN* 3.7 6.7 - - - +
620F LEU* 1.3 75.6 - - - +
622F THR* 1.3 59.3 + - - +
624F ASN* 5.1 0.4 - - - -
625F LEU* 2.9 44.4 + - + +
1669F LEU* 6.5 0.4 - - + -
1673F VAL* 5.1 8.7 - - + -
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Residues in contact with THR 622 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88E PRO* 3.4 29.6 - - + +
89E GLY* 3.4 4.2 - - - -
618F GLN 2.7 22.2 + - - -
619F ASP* 3.7 9.5 + - - -
621F ILE* 1.3 75.8 - - - +
623F GLU* 1.3 56.9 + - - +
626F LEU* 3.6 27.9 - - + +
627F PRO* 3.2 21.7 - - - +
1673F VAL* 4.4 4.4 - - - +
1681F VAL* 3.2 25.8 - - + +
1684F ALA* 4.1 8.3 - - + -
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Residues in contact with GLU 623 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88E PRO* 5.4 7.4 - - + +
89E GLY 4.9 4.0 - - - +
619F ASP 2.9 17.7 + - - +
620F LEU* 3.9 6.7 - - + +
622F THR* 1.3 79.9 - - - +
624F ASN* 1.3 68.0 + - - +
625F LEU 3.6 0.2 - - - -
627F PRO* 3.3 22.9 - - - +
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Residues in contact with ASN 624 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580F GLU* 5.8 1.0 - - - +
583F ILE* 4.6 13.4 - - + +
584F LYS* 6.2 3.4 - - - -
587F ILE* 4.1 33.7 - - + +
620F LEU* 2.9 36.5 + - - +
621F ILE* 3.7 0.9 - - - +
623F GLU* 1.3 84.8 + - - +
625F LEU* 1.3 60.1 + - - +
627F PRO* 4.7 0.9 - - - -
628F GLY* 5.5 2.6 + - - -
631F LEU* 5.4 2.3 - - - +
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Residues in contact with LEU 625 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587F ILE* 5.0 15.9 - - + -
590F LEU* 6.3 2.9 - - + -
603F LEU* 5.4 7.9 - - + -
621F ILE* 2.9 24.3 + - + +
623F GLU 3.6 0.2 - - - -
624F ASN* 1.3 79.7 - - - +
626F LEU* 1.3 85.8 + - + +
627F PRO 3.7 0.9 - - - -
628F GLY* 3.8 8.5 + - - -
629F ARG* 4.1 5.9 + - - -
631F LEU* 5.7 7.5 - - + +
632F LEU* 4.0 30.1 - - + +
1669F LEU* 4.2 23.6 - - + -
1670F TYR* 4.0 19.7 - - + +
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Residues in contact with LEU 626 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E GLY* 3.2 18.4 - - - +
622F THR* 3.6 32.6 + - + +
625F LEU* 1.3 84.2 - - + +
627F PRO* 1.3 70.8 - - + +
628F GLY 3.1 3.5 + - - -
629F ARG* 3.3 24.9 + - - +
1670F TYR* 3.7 33.2 - - + +
1681F VAL* 5.6 2.7 - - + -
1684F ALA* 4.1 12.6 - - + +
1685F LEU* 4.8 3.8 - - + +
1688F HIS* 3.6 35.6 - - + +
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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