Contacts of the helix formed by residues 545 - 560 (chain u) 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 GLU 545 (chain u).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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544u LEU* 1.3 76.8 - - - +
546u ASP* 1.3 54.5 + - - +
547u GLN* 3.3 4.7 - - + +
548u GLU* 3.1 21.1 + - + +
549u ARG* 2.7 36.5 + - - +
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Residues in contact with ASP 546 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545u GLU* 1.3 73.3 - - - +
547u GLN* 1.3 57.4 + - - +
549u ARG* 3.5 6.9 + - - +
550u HIS* 2.9 28.2 + - - +
100y TYR* 4.8 7.5 - - + +
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Residues in contact with GLN 547 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545u GLU* 3.3 4.1 - - + +
546u ASP* 1.3 76.0 - - - +
548u GLU* 1.3 59.2 + - - +
550u HIS* 3.3 4.2 + - - +
551u LEU* 2.9 28.4 + - - +
100y TYR* 4.1 31.2 - - + +
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Residues in contact with GLU 548 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505u LYS* 5.0 19.9 - - + +
544u LEU* 5.4 3.1 - - + -
545u GLU* 3.1 27.4 + - + +
547u GLN* 1.3 77.1 - - - +
549u ARG* 1.3 60.1 + - - +
551u LEU* 3.3 7.4 + - - +
552u LEU* 2.9 28.6 + - - +
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Residues in contact with ARG 549 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539u LEU* 6.4 2.7 - - + -
544u LEU* 5.5 6.4 - - + +
545u GLU 2.7 19.8 + - - +
546u ASP* 3.8 8.3 - - - +
547u GLN 3.3 0.2 - - - -
548u GLU* 1.3 73.7 - - - +
550u HIS* 1.3 58.0 + - - +
552u LEU* 3.3 5.6 + - - +
553u VAL* 2.9 29.8 + - - +
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Residues in contact with HIS 550 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546u ASP 2.9 18.1 + - - +
547u GLN* 3.6 9.0 - - - +
548u GLU 3.3 0.2 - - - -
549u ARG* 1.3 77.1 - - - +
551u LEU* 1.3 56.9 + - - +
553u VAL* 3.5 4.0 + - - +
554u LYS* 2.9 28.2 + - - +
97y ASP* 5.8 8.7 - - + -
100y TYR* 5.0 8.7 - - + -
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Residues in contact with LEU 551 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504u ILE* 4.9 17.0 - - + +
505u LYS* 5.4 5.8 - - - +
547u GLN 2.9 17.1 + - - +
548u GLU* 3.3 7.4 + - - +
550u HIS* 1.3 76.1 - - - +
552u LEU* 1.3 57.7 + - - +
554u LYS* 3.3 8.5 + - - +
555u VAL* 2.9 27.0 + - - +
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Residues in contact with LEU 552 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535u ILE 6.1 0.7 - - - +
539u LEU* 5.5 11.2 - - + -
548u GLU 2.9 17.8 + - - +
549u ARG* 3.8 7.0 - - - +
550u HIS 3.3 0.2 - - - -
551u LEU* 1.3 77.3 - - - +
553u VAL* 1.3 57.1 + - - +
555u VAL* 3.2 10.1 + - - +
556u ILE* 2.9 25.3 + - - +
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Residues in contact with VAL 553 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549u ARG 2.9 17.7 + - - +
550u HIS* 4.2 4.3 - - - +
552u LEU* 1.3 74.5 - - - +
554u LYS* 1.3 60.2 + - - +
556u ILE* 3.6 9.3 - - + +
557u ASP* 2.9 29.6 + - - +
592u GLU* 5.8 8.7 - - + -
596u ILE* 5.6 6.8 - - + +
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Residues in contact with LYS 554 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550u HIS 2.9 19.0 + - - +
551u LEU* 3.3 11.0 - - - +
552u LEU 3.2 0.2 - - - -
553u VAL* 1.3 74.1 - - - +
555u VAL* 1.3 58.9 + - - +
557u ASP* 3.9 1.5 - - - -
558u ARG* 3.0 33.1 + - - +
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Residues in contact with VAL 555 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535u ILE* 6.5 1.3 - - + -
551u LEU 2.9 13.5 + - - +
552u LEU* 3.2 11.6 + - - +
554u LYS* 1.3 75.2 - - - +
556u ILE* 1.3 57.4 + - - +
558u ARG* 3.8 3.2 - - - +
559u ILE* 3.0 31.5 + - - +
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Residues in contact with ILE 556 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552u LEU 2.9 13.2 + - - +
553u VAL* 3.6 13.2 - - + +
554u LYS 3.2 0.4 - - - -
555u VAL* 1.3 78.6 - - - +
557u ASP* 1.3 57.9 + - - +
559u ILE* 3.2 5.5 + - - +
560u LEU* 2.9 25.7 + - - +
596u ILE* 6.0 4.7 - - + -
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Residues in contact with ASP 557 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553u VAL 2.9 17.1 + - - +
554u LYS* 4.7 1.6 - - - +
556u ILE* 1.3 76.6 - - - +
558u ARG* 1.3 60.1 + - - +
560u LEU* 3.6 18.8 + - + +
561u TYR* 3.9 7.8 + - - +
596u ILE* 4.5 22.4 - - + -
599u ASN* 5.9 3.6 - - + -
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Residues in contact with ARG 558 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516u LEU* 6.0 0.9 - - + +
520u THR* 4.2 25.1 - - - -
554u LYS 3.0 19.4 + - - +
555u VAL* 4.2 3.6 - - - +
557u ASP* 1.3 75.9 - - - +
559u ILE* 1.3 59.4 + - - +
561u TYR* 4.2 11.7 + - - +
562u LYS* 4.7 4.0 + - - +
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Residues in contact with ILE 559 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519u ILE 5.8 0.4 - - - +
520u THR* 5.9 0.7 - - - +
523u ALA* 4.4 21.0 - - + +
555u VAL 3.0 17.3 + - - +
556u ILE* 3.6 3.6 - - - +
558u ARG* 1.3 77.6 - - - +
560u LEU* 1.3 61.9 + - - +
561u TYR 3.2 2.0 - - - -
562u LYS* 3.5 4.0 + - - +
563u LEU* 3.2 27.9 + - + +
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Residues in contact with LEU 560 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556u ILE 2.9 15.3 + - - +
557u ASP* 3.6 13.9 + - + +
558u ARG 3.4 0.8 - - - -
559u ILE* 1.3 76.3 - - - +
561u TYR* 1.3 62.8 + - - +
562u LYS 3.5 0.3 + - - -
563u LEU* 3.9 9.1 + - - +
564u ASP* 4.2 10.6 + - - +
599u ASN* 5.0 20.0 - - + +
600u LEU* 5.7 3.8 - - + +
603u ALA* 5.0 6.9 - - - +
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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