Contacts of the helix formed by residues 529 - 539 (chain J) in PDB entry 6C6U
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 GLY 529 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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527J LEU* 3.2 10.4 + - - +
528J THR* 1.3 77.7 - - - +
530J PRO* 1.3 77.2 - - - +
531J LYS* 3.2 5.1 + - - -
532J GLU* 3.7 6.4 + - - +
533J ALA* 3.4 15.4 + - - +
550J VAL* 5.0 5.7 - - - +
551J ARG 3.5 15.5 + - - +
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Residues in contact with PRO 530 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529J GLY* 1.3 82.2 - - - +
531J LYS* 1.3 67.4 + - + +
532J GLU 3.4 0.2 - - - -
533J ALA* 3.2 3.9 + - + +
534J GLU* 3.0 18.4 + - - +
550J VAL* 5.6 0.4 - - + -
551J ARG 3.9 9.4 - - - +
552J ILE* 4.5 8.7 - - + -
577J ALA* 3.3 39.5 - - + +
578J ILE* 4.7 1.7 - - - +
580J TRP* 3.8 25.8 - - + -
581J MET* 3.6 20.8 - - + +
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Residues in contact with LYS 531 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181H GLU* 3.7 35.7 + - + +
182H ARG* 5.1 4.5 - - + +
206H GLU* 2.6 44.5 + - - +
529J GLY* 3.2 2.1 - - - -
530J PRO* 1.3 80.5 - - + +
532J GLU* 1.3 58.7 + - - +
534J GLU* 3.2 6.8 + - - +
535J ARG* 3.0 22.3 + - - +
581J MET* 3.7 26.7 - - + -
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Residues in contact with GLU 532 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86H LYS* 2.4 32.9 + - - -
152H TYR* 2.9 21.0 + - - -
176H CYS* 5.2 1.4 - - - +
181H GLU* 5.2 1.5 - - + +
527J LEU* 3.4 15.4 - - + +
528J THR* 3.3 32.5 + - + +
529J GLY 3.7 9.0 + - - +
531J LYS* 1.3 76.9 - - - +
533J ALA* 1.3 62.5 + - - +
535J ARG* 3.5 36.3 + - - +
536J LEU* 2.8 30.5 + - + +
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Residues in contact with ALA 533 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527J LEU* 3.7 24.0 - - + -
529J GLY 3.4 4.8 + - - -
530J PRO* 3.2 14.1 + - + +
531J LYS 3.2 0.4 - - - -
532J GLU* 1.3 77.6 - - - +
534J GLU* 1.3 57.7 + - - +
536J LEU* 3.3 3.9 + - - +
537J TYR* 3.0 28.1 + - - +
550J VAL* 5.3 0.4 - - + -
574J VAL* 3.8 15.5 - - + +
577J ALA* 3.8 25.4 - - + -
578J ILE* 3.7 6.4 - - + +
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Residues in contact with GLU 534 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182H ARG* 2.4 42.3 + - - +
183H ILE 5.1 6.9 - - - +
184H ALA* 5.2 4.0 - - - +
530J PRO 3.0 11.9 + - - +
531J LYS 3.6 7.9 - - - +
533J ALA* 1.3 75.4 - - - +
535J ARG* 1.3 59.2 + - - +
537J TYR 3.3 0.7 + - - -
538J ARG* 3.0 66.2 + - + +
578J ILE* 3.7 30.8 - - + +
581J MET* 3.3 11.5 - - - +
631J TYR* 4.6 0.2 + - - -
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Residues in contact with ARG 535 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48H LEU* 3.9 37.3 - - + +
152H TYR* 3.3 40.8 - - + +
176H CYS* 3.5 17.7 - - - +
178H SER* 4.1 16.8 + - - -
180H VAL* 2.6 38.4 + - - -
181H GLU* 3.7 31.1 + - - +
531J LYS 3.0 15.8 + - - +
532J GLU* 3.5 25.3 + - - +
533J ALA 3.3 0.2 - - - -
534J GLU* 1.3 78.0 - - - +
536J LEU* 1.3 59.6 + - - +
539J SER* 3.1 24.3 + - - -
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Residues in contact with LEU 536 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152H TYR* 3.6 36.3 - - + +
154H PRO* 5.3 1.3 - - + -
525J MET* 3.8 22.4 - - + -
527J LEU* 3.8 33.7 - - + -
532J GLU* 2.8 20.3 + - - +
533J ALA* 3.7 4.9 - - - +
534J GLU 3.2 0.2 - - - -
535J ARG* 1.3 78.8 - - - +
537J TYR* 1.3 65.5 + - - +
539J SER* 3.5 3.8 + - - -
541J LEU* 3.4 48.7 + - + +
542J ALA* 3.4 19.9 + - + -
574J VAL* 5.7 2.2 - - + -
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Residues in contact with TYR 537 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1222I GLU* 4.2 19.6 + - - -
512J TYR* 6.1 0.2 - - - -
533J ALA 3.0 8.3 + - - +
534J GLU* 4.0 1.1 - - - +
536J LEU* 1.3 76.2 - - - +
538J ARG* 1.3 71.8 + - + +
539J SER 3.2 0.7 + - - -
540J GLY* 3.4 11.1 + - - -
542J ALA* 3.8 19.0 - - - +
543J SER* 5.4 0.4 - - - -
544J LEU* 3.7 42.8 - - + +
574J VAL* 4.3 7.0 - - + -
578J ILE* 3.7 25.6 - - + -
631J TYR* 4.2 30.4 - + - -
634J ARG* 3.3 54.2 + - - +
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Residues in contact with ARG 538 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44H ARG* 4.4 34.2 + - - +
45H ARG* 5.1 5.0 + - - -
48H LEU* 4.1 27.3 - - + +
183H ILE 6.1 0.9 - - - +
1217I THR* 6.0 0.6 - - - +
1219I GLU* 4.1 18.8 - - - +
534J GLU* 3.0 44.8 + - + +
535J ARG 4.0 0.2 + - - -
536J LEU 3.4 0.2 - - - -
537J TYR* 1.3 81.3 - - + +
539J SER* 1.3 58.0 + - - +
540J GLY 3.5 0.4 + - - -
630J ALA* 5.6 3.8 - - - +
631J TYR* 2.8 42.3 + - - -
634J ARG* 3.1 32.7 - - - +
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Residues in contact with SER 539 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45H ARG* 5.9 3.6 - - - +
48H LEU* 3.6 24.2 - - - -
49H SER* 4.5 11.2 - - - -
1219I GLU* 6.0 0.4 - - - -
535J ARG 3.1 14.0 + - - -
536J LEU* 3.5 6.9 + - - -
537J TYR 3.2 0.4 - - - -
538J ARG* 1.3 78.0 - - - +
540J GLY* 1.3 59.1 + - - +
541J LEU* 3.2 28.3 + - - +
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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