Contacts of the helix formed by residues 746 - 755 (chain B) in PDB entry 6RKU
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 746 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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745B MET* 1.3 78.1 - - - +
747B PRO* 1.3 71.2 - - + +
748B GLU* 4.4 15.0 + - + +
749B GLN* 3.3 34.1 + - + +
750B LEU* 2.9 26.7 + - - +
106C GLN* 4.5 18.4 - - - +
107C GLY* 4.3 18.9 + - - +
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Residues in contact with PRO 747 (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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431B SER* 4.1 16.2 - - - +
434B GLN* 4.3 23.1 - - + +
435B GLY* 3.9 29.9 - - - +
745B MET 4.3 2.7 - - - +
746B ASN* 1.3 90.5 - - + +
748B GLU* 1.3 57.2 + - + +
750B LEU* 3.3 8.0 + - + +
751B TRP* 2.9 28.2 + - - +
107C GLY 5.7 5.6 - - - +
108C ASN* 6.0 4.3 - - - +
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Residues in contact with GLU 748 (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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746B ASN* 4.4 16.6 + - + +
747B PRO* 1.3 76.4 - - + +
749B GLN* 1.3 70.9 + - + +
751B TRP* 3.4 7.5 + - - +
752B GLU* 2.9 42.6 + - + +
298C LYS* 5.3 17.7 - - + +
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Residues in contact with GLN 749 (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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536B LYS* 4.6 11.3 - - - +
545B TYR* 4.5 19.5 + - + +
739B TYR* 3.4 23.7 + - - -
745B MET* 3.9 11.3 - - + +
746B ASN* 3.3 43.4 + - + +
748B GLU* 1.3 82.4 + - + +
750B LEU* 1.3 59.5 + - - +
752B GLU* 3.3 8.0 + - - +
753B THR* 2.7 41.6 + - + +
106C GLN* 5.6 2.8 + - - +
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Residues in contact with LEU 750 (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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428B ALA 5.4 0.2 - - - +
431B SER* 3.9 27.1 - - - +
432B ALA* 4.1 21.8 - - + +
435B GLY* 6.1 0.7 - - - -
496B MET* 5.5 4.3 - - + -
742B LEU* 4.4 24.2 - - + +
745B MET* 3.7 27.7 - - + -
746B ASN 2.9 13.8 + - - +
747B PRO 3.3 8.9 + - - +
749B GLN* 1.3 76.3 - - - +
751B TRP* 1.3 63.8 + - - +
753B THR* 3.8 0.4 - - - -
754B THR* 2.9 41.7 + - + +
755B MET* 3.9 16.6 + - + +
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Residues in contact with TRP 751 (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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435B GLY 3.1 26.2 + - - +
436B ARG* 3.6 2.2 - - - -
437B ASN* 3.4 46.0 - - + -
441B GLN* 5.1 7.2 - - + -
747B PRO 2.9 13.9 + - - +
748B GLU* 3.4 11.9 - - - +
750B LEU* 1.3 79.5 - - - +
752B GLU* 1.3 79.5 + - + +
755B MET* 2.9 66.5 + - + -
756B ASP* 3.5 20.6 + - + -
757B PRO* 4.6 14.1 - - + -
298C LYS* 5.0 19.7 - - + +
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Residues in contact with GLU 752 (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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545B TYR* 5.0 7.6 + - - -
748B GLU* 2.9 28.3 + - + +
749B GLN* 4.0 7.5 - - - +
751B TRP* 1.3 92.6 - - + +
753B THR* 1.3 63.2 + - + +
756B ASP* 4.1 10.1 - - - +
759B SER* 3.8 24.1 - - - -
298C LYS* 5.6 5.9 - - - -
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Residues in contact with THR 753 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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531B GLN 4.8 4.5 - - - +
533B PRO* 3.7 28.4 - - + +
545B TYR* 3.8 42.0 - - + +
745B MET* 4.2 7.6 - - - -
749B GLN* 2.7 28.2 + - + +
750B LEU* 3.5 5.9 + - - -
752B GLU* 1.3 82.9 - - + +
754B THR* 1.3 68.6 + - - +
759B SER 5.4 1.5 - - - +
760B ARG* 5.0 8.0 - - - -
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Residues in contact with THR 754 (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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421B TYR* 5.2 3.4 + - + -
496B MET* 3.6 34.8 - - + -
530B ALA* 4.6 12.1 - - + -
531B GLN 5.7 2.0 - - - +
532B PRO* 4.5 12.9 - - + +
533B PRO* 4.3 9.7 - - - +
742B LEU* 5.6 1.4 - - + +
745B MET* 5.6 0.5 - - - +
750B LEU* 2.9 26.2 + - + +
751B TRP 3.1 0.2 + - - -
753B THR* 1.3 91.5 + - - +
755B MET* 1.3 63.2 + - + +
756B ASP 3.6 2.5 - - - -
760B ARG* 3.1 24.6 - - - +
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Residues in contact with MET 755 (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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421B TYR* 4.0 26.7 - - + +
432B ALA* 4.9 8.1 - - + +
435B GLY 4.6 1.1 - - - +
436B ARG* 4.1 22.9 - - - -
441B GLN* 5.2 6.7 + - - +
443B ILE* 6.3 1.1 - - + -
496B MET* 3.9 34.8 - - + -
750B LEU* 4.1 22.4 - - + +
751B TRP* 2.9 62.6 + - + -
754B THR* 1.3 77.2 - - + +
756B ASP* 1.3 58.2 + - - +
757B PRO* 3.8 4.0 - - - +
760B ARG* 4.5 8.3 - - - +
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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