Contacts of the helix formed by residues 643 - 653 (chain B) in PDB entry 6AHU
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 643 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212B PHE* 4.6 4.4 - - - -
223B GLY* 3.4 15.3 - - - -
224B GLU 3.7 11.0 + - - -
226B PRO* 5.4 2.2 - - - +
245B GLN* 4.5 3.2 + - - -
642B GLY* 1.3 75.1 - - - -
644B LEU* 1.3 55.6 + - - -
645B LYS 3.3 2.2 - - - -
646B GLU* 3.5 8.1 - - - +
647B SER* 2.7 33.0 + - - -
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Residues in contact with LEU 644 (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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217B LYS* 3.5 31.2 - - + +
218B TRP* 4.8 14.1 - - + -
222B LEU* 3.7 25.4 - - + -
223B GLY 2.8 18.7 + - - +
224B GLU* 3.3 23.3 + - + +
247B LEU* 6.3 0.2 - - + -
249B TYR* 4.6 14.4 - - + +
643B GLY* 1.3 68.6 - - - -
645B LYS* 1.3 62.2 + - - +
647B SER* 3.1 17.0 + - - +
648B ALA* 2.8 26.2 + - + +
660B PRO* 5.8 5.4 - - + -
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Residues in contact with LYS 645 (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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268A G 2.8 49.2 + - - -
224B GLU* 3.1 24.6 + - + +
225B ARG* 3.7 33.7 - - + +
226B PRO* 6.3 0.7 - - + -
231B HIS* 4.1 20.0 + - - +
644B LEU* 1.3 77.7 - - - +
646B GLU* 1.3 57.4 + - - +
648B ALA* 3.1 10.4 + - + +
649B VAL* 3.1 30.6 + - + +
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Residues in contact with GLU 646 (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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224B GLU 4.4 0.2 + - - -
234B CYS* 3.7 34.6 - - + +
238B MET* 4.1 17.8 - - - +
243B LEU* 3.4 29.7 - - - +
245B GLN* 2.4 37.1 + - - +
435B ILE* 5.2 0.7 - - - +
642B GLY* 3.7 7.3 - - - -
643B GLY 3.2 19.8 + - - +
645B LYS* 1.3 77.7 - - - +
647B SER* 1.3 59.4 + - - +
649B VAL* 3.3 24.5 - - + +
650B HIS* 3.4 8.8 + - - +
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Residues in contact with SER 647 (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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245B GLN* 4.0 19.6 + - - +
247B LEU* 4.5 10.0 - - - +
249B TYR* 4.4 10.9 + - - -
250B TYR* 5.2 2.4 + - - -
433B ARG* 5.5 3.1 + - - -
643B GLY 2.7 18.0 + - - -
644B LEU* 3.1 22.6 + - - +
646B GLU* 1.3 72.8 - - - +
648B ALA* 1.3 58.6 + - - +
650B HIS* 3.7 16.3 - - - +
651B SER* 4.3 3.5 + - - -
658B ASN* 4.1 8.7 + - - -
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Residues in contact with ALA 648 (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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644B LEU* 2.8 11.0 + - + +
645B LYS* 3.1 15.9 + - + +
647B SER* 1.3 75.9 - - - +
649B VAL* 1.3 62.8 + - + +
650B HIS 3.2 1.8 - - - -
651B SER 3.6 1.0 + - - -
652B GLN* 3.5 27.5 + - - +
658B ASN* 3.9 20.5 + - - +
969B GLN* 5.4 0.2 - - - +
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Residues in contact with VAL 649 (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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231B HIS* 4.7 20.6 - - + -
234B CYS* 5.8 2.7 - - + -
235B TYR* 6.2 5.6 - - + +
238B MET* 5.6 4.0 - - - -
614B TRP* 3.3 19.9 - - + -
645B LYS* 3.1 12.5 + - + +
646B GLU* 3.3 33.2 - - + +
648B ALA* 1.3 73.7 - - + +
650B HIS* 1.3 64.5 + - - +
651B SER 3.2 1.9 + - - -
652B GLN* 3.4 26.7 - - - +
653B TYR* 3.7 27.8 + - + +
971B ASP* 5.1 0.7 - - - +
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Residues in contact with HIS 650 (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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238B MET* 3.4 25.6 - - + +
245B GLN* 4.9 4.3 - - - +
433B ARG* 3.8 27.7 + - - -
435B ILE* 3.6 27.0 - - + +
602B GLN* 5.2 3.8 + - - -
614B TRP* 3.2 22.0 - - - -
615B GLY* 4.5 15.3 - - - -
617B GLY* 5.9 1.1 - - - -
646B GLU* 3.4 13.2 + - - +
647B SER* 3.7 17.3 - - - +
648B ALA 3.2 0.6 - - - -
649B VAL* 1.3 79.5 - - - +
651B SER* 1.3 66.5 + - - +
654B LYS* 3.3 27.9 + - - +
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Residues in contact with SER 651 (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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647B SER 4.3 3.0 + - - -
648B ALA 3.6 2.2 + - - -
650B HIS* 1.3 88.5 - - - +
652B GLN* 1.3 60.5 + - - +
653B TYR 3.3 2.0 - - - -
654B LYS* 3.1 11.4 + - - +
655B ARG 2.9 23.9 + - - -
656B SER* 3.0 31.5 + - - +
657B PRO 4.5 5.0 + - - -
658B ASN* 3.4 26.4 + - - -
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Residues in contact with GLN 652 (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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648B ALA* 3.5 18.0 + - - +
649B VAL* 3.4 30.3 - - - +
651B SER* 1.3 78.4 - - - +
653B TYR* 1.3 77.2 + - + +
654B LYS 3.3 0.4 + - - -
655B ARG* 4.0 12.6 + - - +
658B ASN* 5.0 0.2 - - - +
969B GLN* 3.5 42.3 - - + +
970B GLY 4.7 0.3 + - - -
971B ASP* 3.6 33.7 + - - +
980B GLU* 5.3 5.7 - - - +
982B LEU* 4.4 16.3 - - - +
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Residues in contact with TYR 653 (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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231B HIS* 5.2 5.4 + - - -
235B TYR* 4.4 18.4 - + + -
605B LYS* 3.7 19.4 + - - -
614B TRP* 3.6 36.0 - + + -
649B VAL* 3.7 26.4 + - + +
651B SER 3.3 0.4 - - - -
652B GLN* 1.3 101.5 - - + +
654B LYS* 1.3 57.9 + - - +
655B ARG* 3.4 8.8 + - - +
971B ASP* 3.6 16.3 + - + -
972B PHE 2.7 24.5 + - - -
973B SER* 3.6 28.0 - - - -
974B MET* 4.0 20.7 + - + +
975B ALA* 5.3 9.8 - - + +
980B GLU* 5.7 4.7 - - + -
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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