Contacts of the helix formed by residues 548 - 560 (chain A) in PDB entry 4RM9
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A ARG* 3.3 34.6 - - + -
546A LYS 4.7 5.2 - - - +
547A ARG* 1.3 76.9 - - - +
549A HIS* 1.3 64.9 + - - +
550A ASN* 3.7 7.1 + - - +
551A ASP* 2.9 28.1 + - - +
552A ILE* 3.1 24.7 + - - +
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Residues in contact with HIS 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A ASP* 2.8 54.1 + - - -
548A THR* 1.3 73.5 - - - +
550A ASN* 1.3 65.0 + - - +
552A ILE* 3.2 14.9 + - + +
553A ILE* 3.0 58.1 + - + +
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Residues in contact with ASN 550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ASP* 5.5 2.8 + - - -
116A TYR* 3.4 35.2 - - + +
200A MET* 4.7 6.3 - - - +
231A ASP 5.4 0.2 - - - +
233A LYS* 5.2 6.2 + - - +
234A LEU* 3.5 23.7 - - + +
548A THR* 3.3 6.1 + - - +
549A HIS* 1.3 80.4 - - - +
551A ASP* 1.3 59.9 + - - +
553A ILE* 4.2 13.9 - - - +
554A HIS* 2.9 31.2 + - - +
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Residues in contact with ASP 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A TYR* 2.7 32.7 + - - -
119A PRO* 4.4 4.0 - - - +
156A ARG* 3.6 9.1 + - - +
160A GLN* 2.6 37.1 + - - +
547A ARG* 3.6 14.0 - - + -
548A THR* 2.9 33.9 + - - +
550A ASN* 1.3 77.9 - - - +
552A ILE* 1.3 57.4 + - - +
554A HIS* 3.2 2.9 + - - +
555A ASN* 2.8 41.7 + - - +
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Residues in contact with ILE 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547A ARG* 3.6 50.3 - - + +
548A THR 3.1 16.3 + - - +
549A HIS* 3.2 12.8 + - + +
551A ASP* 1.3 75.0 - - - +
553A ILE* 1.3 63.7 - - + +
555A ASN* 3.3 7.9 + - - +
556A GLU* 3.1 24.7 + - + +
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Residues in contact with ILE 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A ASP 3.7 4.5 - - - +
232A ASP* 3.5 46.7 - - + +
234A LEU* 4.0 9.9 - - + -
235A THR* 3.8 10.1 - - - +
549A HIS* 3.0 53.5 + - + +
550A ASN* 3.7 14.1 - - - +
552A ILE* 1.3 75.2 - - + +
554A HIS* 1.3 66.6 + - - +
556A GLU* 3.4 5.9 + - - +
557A ASN* 3.1 27.2 + - - +
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Residues in contact with HIS 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A TYR* 3.6 18.7 - + + +
118A PRO* 3.5 36.9 - - + +
119A PRO* 5.8 0.4 - - + -
199A GLU* 2.6 30.6 + - - -
234A LEU* 4.0 6.5 - - + -
550A ASN 2.9 19.8 + - - +
551A ASP 3.5 3.1 - - - +
553A ILE* 1.3 77.7 - - - +
555A ASN* 1.3 70.7 + - - +
557A ASN* 3.3 7.1 + - - +
558A MET* 2.9 63.4 + - + +
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Residues in contact with ASN 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A TYR* 5.3 0.2 + - - -
542A ARG* 5.0 11.7 + - - +
547A ARG* 4.6 16.2 - - - +
551A ASP* 2.8 28.2 + - - +
552A ILE* 3.8 7.7 - - - +
553A ILE 3.2 0.2 - - - -
554A HIS* 1.3 89.4 - - - +
556A GLU* 1.3 59.6 + - - +
558A MET* 3.3 8.9 + - - +
559A ARG* 2.8 28.1 + - - +
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Residues in contact with GLU 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552A ILE* 3.1 17.9 + - + +
553A ILE* 3.8 5.8 - - - +
555A ASN* 1.3 75.3 - - - +
557A ASN* 1.3 64.7 + - - +
559A ARG* 2.9 47.7 + - - +
560A GLN* 3.0 52.5 + - - +
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Residues in contact with ASN 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A GLU* 4.9 7.8 + - - +
234A LEU* 4.6 6.5 + - - +
235A THR* 2.7 42.8 + - - +
553A ILE* 3.1 25.3 + - - +
554A HIS* 3.4 12.2 - - - +
555A ASN 3.3 0.2 - - - -
556A GLU* 1.3 79.6 - - - +
558A MET* 1.3 61.6 + - + +
560A GLN* 3.1 15.3 + - - +
561A GLY 3.3 0.2 + - - -
562A ARG* 3.0 48.0 + - + +
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Residues in contact with MET 558 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554A HIS* 2.9 51.5 + - + +
555A ASN* 3.5 9.6 - - - +
557A ASN* 1.3 74.8 - - - +
559A ARG* 1.3 60.7 + - - +
561A GLY* 2.8 21.6 + - - +
562A ARG 3.8 18.4 - - - +
563A ASP* 5.8 1.8 - - - -
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Residues in contact with ARG 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555A ASN 2.8 14.3 + - - +
556A GLU* 2.9 46.8 + - - +
558A MET* 1.3 75.5 - - - +
560A GLN* 1.3 64.2 + - - +
561A GLY* 3.1 3.7 + - - -
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Residues in contact with GLN 560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556A GLU* 3.0 49.8 + - - +
557A ASN* 3.4 12.5 + - - +
558A MET 3.0 0.4 - - - -
559A ARG* 1.3 84.6 - - - +
561A GLY* 1.3 60.1 + - - +
562A ARG* 3.1 35.0 + - + +
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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