Contacts of the helix formed by residues 548 - 559 (chain C) in PDB entry 6NID
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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507C MET* 4.9 3.8 - - - -
547C GLN* 1.3 76.1 - - - +
549C VAL* 1.3 61.4 + - - +
550C GLU* 3.5 10.4 + - - +
551C GLN* 2.9 39.8 + - - +
552C LEU* 2.9 25.8 + - - +
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Residues in contact with VAL 549 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505C LEU* 4.0 24.9 - - + +
506C LYS* 4.8 2.7 - - - +
507C MET* 4.5 28.6 - - + +
513C CYS* 5.2 2.7 - - - -
547C GLN 3.9 0.6 + - - -
548C THR* 1.3 73.8 - - - +
550C GLU* 1.3 58.4 + - - +
552C LEU* 3.2 15.9 + - + +
553C GLN* 2.8 27.9 + - - +
1475F TYR* 3.3 52.7 - - + +
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Residues in contact with GLU 550 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548C THR* 3.2 9.2 + - - +
549C VAL* 1.3 82.4 - - - +
551C GLN* 1.3 62.3 + - + +
553C GLN* 3.3 8.8 + - - +
554C LYS* 3.1 22.6 + - + +
1475F TYR* 3.9 27.6 - - + +
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Residues in contact with GLN 551 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546C ASN 4.5 2.9 + - - +
547C GLN* 3.6 25.9 + - - +
548C THR* 2.9 49.6 + - - +
550C GLU* 1.3 76.2 - - + +
552C LEU* 1.3 57.7 + - - +
554C LYS* 3.3 8.4 + - - +
555C MET* 2.9 30.9 + - - +
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Residues in contact with LEU 552 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505C LEU* 5.2 5.6 - - + -
507C MET* 5.7 2.0 - - + -
513C CYS* 4.1 22.0 - - + -
539C ILE* 4.3 6.1 - - + -
542C ILE* 5.9 0.7 - - + -
544C VAL* 3.8 40.2 - - + +
547C GLN* 3.7 26.2 - - + +
548C THR 2.9 17.9 + - - +
549C VAL* 3.5 18.2 - - + +
551C GLN* 1.3 76.9 - - - +
553C GLN* 1.3 58.6 + - - +
555C MET* 3.7 22.6 - - + +
556C LEU* 2.8 42.2 + - + +
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Residues in contact with GLN 553 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505C LEU* 6.0 0.4 - - - +
549C VAL* 2.8 13.6 + - + +
550C GLU* 3.5 13.0 - - - +
551C GLN 3.2 0.2 - - - -
552C LEU* 1.3 76.4 - - - +
554C LYS* 1.3 56.9 + - - +
556C LEU* 3.3 1.9 + - - +
557C ARG* 2.8 63.3 + - - +
1475F TYR* 3.5 27.1 - - + +
1476F TYR* 2.9 39.3 + - - +
1477F VAL* 3.7 17.0 - - + +
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Residues in contact with LYS 554 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550C GLU* 3.1 13.4 + - + +
551C GLN* 3.7 10.1 - - - +
553C GLN* 1.3 76.4 - - - +
555C MET* 1.3 63.4 + - - +
557C ARG* 3.3 10.7 + - - +
558C GLU* 3.3 23.2 + - + +
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Residues in contact with MET 555 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539C ILE* 4.0 31.9 - - + -
542C ILE* 3.9 34.5 - - + -
547C GLN* 4.7 12.6 - - - +
551C GLN 2.9 17.4 + - - +
552C LEU* 3.7 16.2 - - + +
554C LYS* 1.3 77.4 - - - +
556C LEU* 1.3 64.0 + - + +
558C GLU* 3.3 4.8 + - - +
559C MET* 3.1 54.4 + - + +
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Residues in contact with LEU 556 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495C LYS* 3.2 24.0 - - + +
501C MET* 4.0 20.6 - - + +
505C LEU* 3.9 28.3 - - + -
539C ILE* 3.8 40.4 - - + -
552C LEU* 2.8 24.2 + - + +
553C GLN 3.9 3.1 - - - +
555C MET* 1.3 75.1 - - + +
557C ARG* 1.3 62.1 + - - +
558C GLU 3.4 0.3 + - - -
559C MET* 3.5 16.7 + - + +
563C ILE* 4.4 6.5 - - + -
565C PHE* 4.3 8.3 - - + -
1477F VAL* 4.0 27.8 - - + +
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Residues in contact with ARG 557 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495C LYS* 3.8 7.3 + - - +
498C ASP* 5.8 0.3 - - - +
500C PRO* 6.3 1.4 - - - +
553C GLN* 2.8 46.3 + - - +
554C LYS* 3.5 10.9 - - - +
555C MET 3.2 0.2 - - - -
556C LEU* 1.3 78.3 - - - +
558C GLU* 1.3 57.6 + - - +
560C ARG* 3.0 22.7 + - - -
1476F TYR* 2.7 37.8 + - - +
1477F VAL* 4.4 6.7 - - - +
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Residues in contact with GLU 558 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554C LYS* 3.3 14.0 + - + +
555C MET* 4.1 4.0 - - - +
556C LEU 3.3 0.4 - - - -
557C ARG* 1.3 75.4 - - + +
559C MET* 1.3 66.3 + - - +
560C ARG* 3.4 15.3 + - - +
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Residues in contact with MET 559 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495C LYS* 3.2 17.1 - - + +
539C ILE* 4.1 21.1 - - + -
540C ASN* 4.6 11.0 - - + +
542C ILE* 4.2 13.9 - - + -
555C MET* 3.1 52.1 + - + +
556C LEU* 3.9 17.3 - - + +
557C ARG 3.4 1.2 - - - -
558C GLU* 1.3 75.9 - - - +
560C ARG* 1.3 75.4 + - - +
563C ILE* 3.8 26.2 - - + -
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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