Contacts of the helix formed by residues 551 - 561 (chain A) in PDB entry 1LMU
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 551 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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539A SER* 2.6 30.9 + - - +
540A PHE 2.9 14.7 + - - +
541A LEU 3.7 4.5 - - - +
542A THR* 2.8 29.6 - - - +
550A SER* 1.3 76.3 - - - +
552A ASP* 1.4 57.8 + - - +
553A ALA* 3.4 3.7 + - - +
554A GLY 3.0 12.6 + - - -
555A LYS* 2.7 36.0 + - - +
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Residues in contact with ASP 552 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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551A THR* 1.4 74.7 - - - +
553A ALA* 1.3 58.1 + - - +
555A LYS* 3.3 11.7 + - - +
556A ALA* 2.8 30.9 + - - +
617A ILE* 4.7 10.3 - - + +
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Residues in contact with ALA 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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189A TYR* 4.0 14.8 - - + +
193A LEU* 5.3 1.1 - - + +
539A SER* 4.1 10.8 - - - +
540A PHE* 4.0 9.8 - - + -
551A THR* 3.2 8.5 + - - +
552A ASP* 1.3 79.0 - - - +
554A GLY* 1.3 62.8 + - - +
556A ALA* 3.6 1.4 - - - +
557A LEU* 2.9 25.5 + - - +
617A ILE* 3.3 38.3 - - + +
618A VAL 4.8 3.4 - - - +
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Residues in contact with GLY 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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203A LEU* 3.8 12.8 - - - +
207A VAL* 4.6 1.1 - - - -
540A PHE* 3.5 31.2 - - - -
550A SER* 5.1 0.4 - - - -
551A THR* 3.0 17.8 + - - -
553A ALA* 1.3 77.8 - - - +
555A LYS* 1.3 61.3 + - - +
557A LEU* 3.3 3.1 + - - +
558A ILE* 3.0 22.9 + - - +
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Residues in contact with LYS 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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207A VAL* 4.0 17.1 + - + -
210A ASP* 3.3 32.8 + - - +
211A GLU* 3.9 18.4 - - - +
214A GLU* 6.6 0.2 - - - -
550A SER* 3.4 22.3 + - - +
551A THR 2.7 23.5 + - - +
552A ASP* 3.8 10.5 - - - +
554A GLY* 1.3 72.9 - - - +
556A ALA* 1.3 61.5 + - - +
558A ILE* 2.7 27.0 - - - +
559A HIS* 2.8 22.9 + - + +
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Residues in contact with ALA 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 ASP 2.8 18.4 + - - +
553A ALA 3.6 1.1 - - - +
555A LYS* 1.3 74.1 - - - +
557A LEU* 1.3 56.6 + - - +
559A HIS* 3.4 5.7 + - - +
560A SER* 2.7 32.7 + - - -
613A ARG* 4.4 15.1 - - + +
614A PHE* 5.0 3.4 - - + -
617A ILE* 3.2 36.8 - - + -
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Residues in contact with LEU 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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180A TYR* 4.3 20.4 - - + -
193A LEU* 4.0 29.6 - - + -
194A SER 3.5 23.3 - - - +
195A VAL* 4.6 1.8 - - + -
200A THR* 4.6 9.9 - - + -
203A LEU* 5.2 8.1 - - + -
535A LEU* 6.5 0.2 - - + -
540A PHE* 3.8 29.2 - - + -
553A ALA 2.9 16.7 + - - +
554A GLY 3.6 4.3 - - - +
556A ALA* 1.3 74.4 - - - +
558A ILE* 1.3 59.9 + - - +
560A SER* 3.0 15.4 + - - -
561A LEU* 2.7 39.5 + - + +
614A PHE* 4.7 4.7 - - + -
617A ILE* 5.2 0.4 - - - +
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Residues in contact with ILE 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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200A THR 6.0 0.4 - - - +
203A LEU* 4.3 4.7 - - + +
204A GLY* 3.3 30.3 - - - +
207A VAL* 3.2 44.4 - - + -
208A ARG* 4.8 7.0 - - + +
554A GLY 3.0 10.9 + - - +
555A LYS* 2.7 28.9 - - - +
557A LEU* 1.3 77.6 - - - +
559A HIS* 1.3 72.5 + - + +
561A LEU* 3.1 28.1 + - + +
566A ALA* 4.3 20.1 - - + +
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Residues in contact with HIS 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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207A VAL* 4.7 1.3 - - + +
211A GLU* 3.6 32.1 + - - -
555A LYS* 2.8 36.6 + - + +
556A ALA* 4.0 5.7 - - - +
557A LEU 3.3 0.2 - - - -
558A ILE* 1.3 90.8 - - + +
560A SER* 1.3 60.1 + - - +
561A LEU 3.5 6.4 + - - +
613A ARG* 4.0 31.1 + - - +
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Residues in contact with SER 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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180A TYR* 4.1 14.2 + - - -
556A ALA 2.7 19.1 + - - -
557A LEU* 3.0 9.5 + - - -
559A HIS* 1.3 78.1 - - - +
561A LEU* 1.3 59.3 + - - +
562A PRO* 4.1 2.3 - - - +
609A THR* 4.3 20.8 + - - +
613A ARG* 4.6 15.4 - - - +
614A PHE* 3.0 39.7 - - - -
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Residues in contact with LEU 561 (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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176A MET* 4.5 0.2 - - + -
180A TYR* 3.5 28.9 - - + +
195A VAL* 3.6 26.9 - - + -
200A THR* 4.6 9.2 - - + -
557A LEU* 2.7 47.8 - - + +
558A ILE* 3.1 24.0 + - + +
559A HIS 3.6 6.1 - - - +
560A SER* 1.3 80.5 - - - +
562A PRO* 1.3 79.7 - - + +
563A GLU* 4.8 3.8 - - - +
565A ALA* 3.5 23.6 - - + -
566A ALA* 5.1 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