Contacts of the helix formed by residues 615 - 626 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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613B ALA 4.7 0.9 - - - -
614B VAL* 1.3 79.1 - - - +
616B SER* 1.3 62.0 + - - +
617B ASN 3.5 0.4 - - - -
618B GLN* 4.0 5.5 - - - +
619B ASP* 3.1 35.3 + - - +
1678B ASN* 4.2 17.9 - - - +
2169B VAL* 4.5 20.2 - - - -
2170B GLN* 5.1 1.5 + - - -
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Residues in contact with SER 616 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578B ILE* 5.9 2.4 - - - +
614B VAL* 4.7 6.8 - - - +
615B CYS* 1.3 76.7 + - - +
617B ASN* 1.3 61.1 + - - +
619B ASP* 3.3 5.3 + - - +
620B LEU* 2.9 40.7 + - - +
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Residues in contact with ASN 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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578B ILE* 4.0 26.0 - - + -
583B ILE* 4.4 4.2 - - + +
606B LEU* 4.0 17.9 - - + +
607B CYS* 5.0 2.9 - - - +
614B VAL* 3.9 19.3 - - + +
615B CYS 3.5 0.2 - - - -
616B SER* 1.3 81.9 + - - +
618B GLN* 1.3 56.4 + - - +
620B LEU* 3.3 9.8 + - - +
621B ILE* 2.9 30.3 + - - +
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Residues in contact with GLN 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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607B CYS* 3.4 41.5 + - - +
608B VAL* 5.3 2.4 - - - +
613B ALA* 4.6 13.7 - - - +
614B VAL 3.4 20.3 + - - +
615B CYS 3.7 3.9 + - - +
616B SER 3.3 0.4 - - - -
617B ASN* 1.3 75.9 - - - +
619B ASP* 1.3 58.3 + - - +
621B ILE* 3.3 5.9 + - - +
622B THR* 2.7 35.6 + - - +
1672B ALA 4.5 3.2 + - - -
1673B VAL* 2.9 30.2 + - + +
1675B ALA 4.8 5.3 + - - -
1678B ASN* 2.4 37.0 + - - +
1681B VAL* 4.3 3.6 - - + +
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Residues in contact with ASP 619 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A PRO* 5.6 9.5 - - - +
615B CYS* 3.1 23.5 + - - +
616B SER* 3.8 4.9 - - - +
618B GLN* 1.3 76.6 - - - +
620B LEU* 1.3 59.1 + - + +
622B THR* 3.3 8.9 + - - -
623B GLU* 2.9 30.5 + - - +
1678B ASN* 5.8 0.7 + - - +
1680B ARG* 3.9 35.1 + - - +
1681B VAL* 5.6 4.9 - - - +
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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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578B ILE* 6.3 2.5 - - + -
579B GLN* 4.2 5.2 - - - +
580B GLU* 3.8 41.3 - - + +
583B ILE* 3.7 19.7 - - + -
616B SER* 2.9 26.8 + - - +
617B ASN* 3.7 7.6 - - - +
619B ASP* 1.3 78.4 - - + +
621B ILE* 1.3 57.6 + - - +
623B GLU* 3.3 4.7 + - + -
624B ASN* 2.9 44.9 + - - +
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Residues in contact with ILE 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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583B ILE* 3.5 15.8 - - + +
587B ILE* 6.4 0.7 - - - -
603B LEU* 4.9 13.5 - - + -
617B ASN 2.9 17.4 + - - +
618B GLN* 3.7 7.0 - - - +
619B ASP 3.3 0.2 - - - -
620B LEU* 1.3 75.0 - - - +
622B THR* 1.3 58.1 + - - +
624B ASN* 5.1 0.7 - - - -
625B LEU* 2.9 44.4 + - + +
1669B LEU* 6.5 0.9 - - + -
1673B VAL* 5.1 9.0 - - + -
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Residues in contact with THR 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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88A PRO* 3.4 29.4 - - + +
89A GLY* 3.4 4.7 - - - -
618B GLN 2.7 21.5 + - - -
619B ASP* 3.7 9.1 + - - -
621B ILE* 1.3 77.4 - - - +
623B GLU* 1.3 57.3 + - - +
626B LEU* 3.6 28.5 - - + +
627B PRO* 3.2 21.5 - - - +
1673B VAL* 4.4 4.9 - - - +
1681B VAL* 3.2 26.2 - - + +
1684B ALA* 4.1 7.9 - - + -
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Residues in contact with GLU 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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88A PRO* 5.4 7.6 - - + +
89A GLY 4.9 3.8 - - - +
619B ASP 2.9 17.5 + - - +
620B LEU* 3.9 7.0 - - + +
621B ILE 3.2 0.2 - - - -
622B THR* 1.3 78.8 - - - +
624B ASN* 1.3 67.5 + - - +
625B LEU 3.6 0.2 - - - -
627B PRO* 3.3 22.4 - - - +
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Residues in contact with ASN 624 (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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580B GLU* 5.8 1.0 - - - +
583B ILE* 4.6 13.2 - - + +
584B LYS* 6.2 4.0 - - - -
587B ILE* 4.1 33.0 - - + +
620B LEU* 2.9 36.2 + - - +
621B ILE 3.7 0.4 - - - -
623B GLU* 1.3 86.1 + - - +
625B LEU* 1.3 58.9 + - - +
627B PRO* 4.7 0.9 - - - -
628B GLY* 5.5 3.4 + - - -
631B LEU* 5.4 2.6 - - - +
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Residues in contact with LEU 625 (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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587B ILE* 5.0 16.8 - - + -
590B LEU* 6.3 3.1 - - + -
603B LEU* 5.4 7.4 - - + -
621B ILE* 2.9 26.0 + - + +
624B ASN* 1.3 80.3 - - - +
626B LEU* 1.3 84.7 + - + +
627B PRO 3.7 0.4 - - - -
628B GLY* 3.8 8.4 + - - -
629B ARG 4.1 5.7 + - - -
631B LEU* 5.7 8.3 - - + +
632B LEU* 4.0 30.3 - - + +
1669B LEU* 4.2 23.8 - - + -
1670B TYR* 4.0 19.3 - - + +
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Residues in contact with LEU 626 (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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89A GLY* 3.2 18.8 - - - +
622B THR* 3.6 32.8 + - + +
625B LEU* 1.3 84.1 - - + +
627B PRO* 1.3 69.1 - - + +
628B GLY 3.1 3.9 + - - -
629B ARG* 3.3 25.5 + - - +
1670B TYR* 3.7 32.3 - - + +
1681B VAL* 5.6 2.5 - - + -
1684B ALA* 4.1 12.3 - - + +
1685B LEU* 4.8 4.0 - - + +
1688B HIS* 3.6 35.2 - - + +
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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