Contacts of the helix formed by residues 548 - 558 (chain 8) in PDB entry 6FF7
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 THR 548 (chain 8).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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506 A 4.6 11.7 - - - -
5468 GLN 3.8 2.2 + - - -
5478 LYS* 1.3 75.7 - - - +
5498 MET* 1.3 62.0 + - - +
5508 LYS* 3.2 10.3 - - - -
5518 SER* 3.3 8.0 + - - -
5528 LYS* 2.9 28.4 + - - +
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Residues in contact with MET 549 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506 A 4.0 32.7 + - - +
516 U 4.3 2.5 + - - -
157 GLY 5.0 0.7 - - - +
5488 THR* 1.3 74.3 - - - +
5508 LYS* 1.3 61.5 + - - +
5528 LYS* 4.2 7.8 - - - +
5538 MET* 2.9 30.8 + - - +
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Residues in contact with LYS 550 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456 A 5.7 5.8 - - + +
466 G 5.7 4.3 - - - +
506 A 5.6 0.8 + - - -
516 U 3.4 27.9 + - - +
137 SER 4.1 4.9 - - - +
157 GLY 5.8 0.2 - - - -
5488 THR* 3.2 7.4 - - - -
5498 MET* 1.3 78.2 - - - +
5518 SER* 1.3 57.8 + - - +
5538 MET* 3.4 3.4 + - - +
5548 ARG* 2.9 28.2 + - - +
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Residues in contact with SER 551 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456 A 5.0 11.4 - - - -
5478 LYS* 4.1 18.2 - - - -
5488 THR* 3.3 12.7 + - - +
5508 LYS* 1.3 80.0 - - - +
5528 LYS* 1.3 58.2 + - - +
5548 ARG* 3.0 7.2 + - - +
5558 GLU* 2.9 33.8 + - - +
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Residues in contact with LYS 552 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5478 LYS* 4.8 7.1 - - + +
5488 THR 2.9 18.3 + - - +
5498 MET* 3.7 7.9 - - - +
5508 LYS 3.4 0.4 - - - -
5518 SER* 1.3 75.8 - - - +
5538 MET* 1.3 57.4 + - - +
5558 GLU* 5.7 0.4 - - - -
5568 LYS* 3.2 20.5 + - - +
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Residues in contact with MET 553 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137 SER 4.0 6.5 - - - +
147 GLY* 3.9 17.6 - - - +
157 GLY 3.5 27.1 - - - +
167 VAL* 5.0 4.3 - - - -
177 ALA* 5.4 4.5 - - + +
5498 MET 2.9 18.6 + - - +
5508 LYS* 4.0 3.4 - - - +
5528 LYS* 1.3 78.0 - - - +
5548 ARG* 1.3 63.1 + - - +
5568 LYS* 3.7 7.5 - - - +
5578 VAL* 3.6 12.6 + - - +
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Residues in contact with ARG 554 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446 G 5.4 13.5 - - + +
127 GLY 4.7 9.0 - - - +
137 SER 3.9 10.8 - - - +
147 GLY* 5.3 0.2 - - - -
5508 LYS 2.9 17.6 + - - +
5518 SER* 3.0 9.6 + - - +
5538 MET* 1.3 75.0 - - - +
5558 GLU* 1.3 52.2 + - - +
5568 LYS 3.1 3.1 - - - -
5578 VAL* 3.2 3.5 + - - +
5588 ARG* 2.6 41.8 + - + +
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Residues in contact with GLU 555 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5518 SER 2.9 15.9 + - - +
5528 LYS* 5.7 0.9 - - - -
5548 ARG* 1.3 70.6 - - - +
5568 LYS* 1.3 61.8 + - - +
5588 ARG 3.4 16.8 - - - +
5598 PRO* 3.4 23.0 - - + +
5608 LYS* 5.0 4.0 - - + +
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Residues in contact with LYS 556 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5528 LYS 3.2 26.0 + - - +
5538 MET* 3.7 10.3 - - - +
5548 ARG 3.1 1.0 - - - -
5558 GLU* 1.3 79.1 - - - +
5578 VAL* 1.3 59.6 + - + +
5598 PRO* 4.9 2.3 - - - +
1056u MET 5.0 0.3 - - - +
1057u ARG* 4.3 12.0 - - - +
1060u PHE* 3.6 28.6 - - + +
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Residues in contact with VAL 557 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147 GLY* 4.9 13.2 - - - +
5538 MET 3.6 10.4 + - - +
5548 ARG 3.2 3.0 + - - +
5568 LYS* 1.3 77.9 - - + +
5588 ARG* 1.3 61.3 + - - +
5598 PRO 3.8 1.3 - - - -
207t GLU 5.4 0.3 - - - +
208t THR* 4.3 30.5 - - - +
210t PHE* 5.3 10.5 - - + -
1057u ARG* 3.9 20.9 - - - +
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Residues in contact with ARG 558 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446 G 4.5 16.6 - - - +
5548 ARG* 2.6 21.1 + - + +
5558 GLU* 3.4 13.1 - - - +
5578 VAL* 1.3 74.1 - - - +
5598 PRO* 1.3 63.4 - - - +
5608 LYS 3.9 0.2 + - - -
208t THR* 5.8 4.3 - - - -
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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