Contacts of the helix formed by residues 615 - 626 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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613D ALA 4.7 0.9 - - - -
614D VAL* 1.3 79.1 - - - +
616D SER* 1.3 59.8 + - - +
617D ASN 3.5 0.7 - - - -
618D GLN* 4.0 5.4 - - - +
619D ASP* 3.1 35.8 + - - +
1678D ASN* 4.2 18.2 - - - +
2169D VAL* 4.5 21.3 - - - -
2170D GLN* 5.1 1.7 + - - -
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Residues in contact with SER 616 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578D ILE* 5.9 2.6 - - - +
614D VAL* 4.7 6.6 - - - +
615D CYS* 1.3 75.6 + - - +
617D ASN* 1.3 62.5 + - - +
619D ASP* 3.3 4.5 + - - +
620D LEU* 2.9 40.0 + - - +
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Residues in contact with ASN 617 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578D ILE* 4.0 25.6 - - + -
583D ILE* 4.4 3.5 - - + +
606D LEU* 4.0 17.3 - - + +
607D CYS* 5.0 3.6 - - - +
614D VAL* 3.9 19.6 - - + +
615D CYS 3.5 0.2 - - - -
616D SER* 1.3 80.6 + - - +
618D GLN* 1.3 57.8 + - - +
620D LEU* 3.3 9.2 + - - +
621D ILE* 2.9 29.9 + - - +
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Residues in contact with GLN 618 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607D CYS* 3.4 40.9 + - - +
608D VAL* 5.3 2.4 - - - +
613D ALA* 4.6 13.9 - - - +
614D VAL 3.4 19.7 + - - +
615D CYS 3.7 4.1 + - - +
616D SER 3.3 0.4 - - - -
617D ASN* 1.3 76.5 - - - +
619D ASP* 1.3 60.6 + - - +
621D ILE* 3.3 6.3 + - - +
622D THR* 2.7 34.8 + - - +
1672D ALA 4.5 2.8 + - - -
1673D VAL* 2.9 30.6 + - + +
1675D ALA 4.8 6.3 + - - -
1678D ASN* 2.4 37.4 + - - +
1681D VAL* 4.3 4.1 - - + +
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Residues in contact with ASP 619 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C PRO* 5.6 9.6 - - - +
615D CYS* 3.1 23.7 + - - +
616D SER* 3.8 5.2 - - - +
618D GLN* 1.3 76.4 - - - +
620D LEU* 1.3 58.9 + - + +
622D THR* 3.3 8.0 + - - -
623D GLU* 2.9 30.5 + - - +
1678D ASN* 5.8 0.9 + - - +
1680D ARG* 3.9 35.0 + - - +
1681D VAL* 5.6 5.4 - - - +
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Residues in contact with LEU 620 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578D ILE* 6.3 2.2 - - + -
579D GLN* 4.2 5.4 - - - +
580D GLU* 3.8 39.9 - - + +
583D ILE* 3.7 19.7 - - + -
616D SER* 2.9 28.6 + - - +
617D ASN* 3.7 7.9 - - - +
619D ASP* 1.3 78.6 - - + +
621D ILE* 1.3 56.6 + - - +
623D GLU* 3.3 4.8 + - + -
624D ASN* 2.9 45.4 + - - +
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Residues in contact with ILE 621 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583D ILE* 3.5 15.8 - - + +
587D ILE* 6.4 0.7 - - - -
603D LEU* 4.9 13.0 - - + -
617D ASN 2.9 17.6 + - - +
618D GLN* 3.7 5.8 - - - +
620D LEU* 1.3 75.4 - - - +
622D THR* 1.3 58.7 + - - +
624D ASN* 5.1 0.9 - - - -
625D LEU* 2.9 45.4 + - + +
1669D LEU* 6.5 0.7 - - + -
1673D VAL* 5.1 8.7 - - + -
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Residues in contact with THR 622 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C PRO* 3.4 29.6 - - + +
89C GLY* 3.4 4.0 - - - -
618D GLN 2.7 22.7 + - - -
619D ASP* 3.3 9.6 + - - -
621D ILE* 1.3 76.9 - - - +
623D GLU* 1.3 57.1 + - - +
626D LEU* 3.6 27.0 - - + +
627D PRO* 3.2 21.0 - - - +
1673D VAL* 4.4 4.6 - - - +
1681D VAL* 3.2 25.7 - - + +
1684D ALA* 4.1 8.7 - - + -
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Residues in contact with GLU 623 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C PRO* 5.4 8.0 - - + -
89C GLY 4.9 4.0 - - - +
619D ASP 2.9 17.9 + - - +
620D LEU* 3.9 7.2 - - + +
622D THR* 1.3 79.6 - - - +
624D ASN* 1.3 66.0 + - - +
625D LEU 3.6 0.2 - - - -
627D PRO* 3.3 23.1 - - - +
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Residues in contact with ASN 624 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580D GLU* 5.8 1.2 - - - +
583D ILE* 4.6 13.1 - - + +
584D LYS* 6.2 3.6 - - - -
587D ILE* 4.1 32.8 - - + +
620D LEU* 2.9 37.9 + - - +
621D ILE* 3.7 0.7 - - - +
623D GLU* 1.3 85.2 + - - +
625D LEU* 1.3 59.2 + - - +
627D PRO* 4.7 1.1 - - - -
628D GLY* 5.5 3.1 + - - -
631D LEU* 5.4 2.3 - - - +
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Residues in contact with LEU 625 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587D ILE* 5.0 15.7 - - + -
590D LEU* 6.3 3.1 - - + -
603D LEU* 5.4 7.2 - - + -
621D ILE* 2.9 26.4 + - + +
623D GLU 3.6 0.2 - - - -
624D ASN* 1.3 80.1 - - - +
626D LEU* 1.3 85.6 + - + +
627D PRO 3.7 0.9 - - - -
628D GLY* 3.8 7.7 + - - -
629D ARG* 4.1 6.2 + - - -
631D LEU* 5.7 7.6 - - + +
632D LEU* 4.0 30.4 - - + +
1669D LEU* 4.2 23.6 - - + -
1670D TYR* 4.0 19.7 - - + +
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Residues in contact with LEU 626 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C GLY* 3.2 17.9 - - - +
622D THR* 3.6 33.7 + - + +
625D LEU* 1.3 83.4 - - + +
627D PRO* 1.3 71.0 - - + +
628D GLY 3.1 3.2 + - - -
629D ARG* 3.3 25.6 + - - +
1670D TYR* 3.7 33.2 - - + +
1681D VAL* 5.6 2.2 - - + -
1684D ALA* 4.1 12.8 - - + +
1685D LEU* 4.8 3.8 - - - +
1688D HIS* 3.6 35.0 - - + +
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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