Contacts of the helix formed by residues 554 - 564 (chain A) in PDB entry 4N41
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 PHE 554 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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477A PHE* 3.7 39.5 - + + -
485A PHE* 3.9 22.9 - + - -
519A VAL* 3.6 27.4 - - + -
543A LEU* 5.3 4.9 - - + -
545A ARG* 3.5 47.1 - - + -
549A VAL* 4.0 6.1 - - + -
550A PRO 4.8 0.4 - - - -
551A GLN 3.1 12.9 + - - +
552A ASP 2.9 1.4 - - - -
553A GLU* 1.3 85.4 - - + +
555A ALA* 1.3 63.5 + - - +
556A LEU 3.4 2.9 - - - -
557A ALA* 3.2 8.5 + - + +
558A LEU* 3.1 27.0 + - + +
570A LEU* 4.0 27.4 - - + -
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Residues in contact with ALA 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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516A GLN* 3.7 10.8 - - - +
551A GLN 4.1 1.6 + - - -
552A ASP* 3.0 21.1 + - - +
553A GLU 3.5 0.4 - - - -
554A PHE* 1.3 76.7 - - - +
556A LEU* 1.3 63.7 + - - +
558A LEU* 3.3 6.0 + - - +
559A GLU* 2.9 28.1 + - - +
91B TYR* 3.7 32.8 + - + -
93B LYS* 4.0 11.2 - - - +
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Residues in contact with LEU 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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516A GLN* 3.6 45.6 + - + +
517A GLU* 4.0 23.1 - - + +
520A TRP* 4.0 22.0 - - + -
554A PHE 3.4 0.6 - - - -
555A ALA* 1.3 77.9 - - - +
557A ALA* 1.3 58.8 + - - +
559A GLU* 3.3 5.9 + - + -
560A ALA* 2.9 33.2 + - + +
563A ARG* 3.6 25.6 - - - +
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Residues in contact with ALA 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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477A PHE* 5.9 0.4 - - + -
516A GLN 4.9 0.8 + - - -
519A VAL* 4.1 24.5 - - + -
520A TRP* 3.9 21.6 - - - +
523A LEU* 3.9 20.5 - - + +
543A LEU* 5.5 1.3 - - + -
554A PHE* 3.2 13.6 + - + +
556A LEU* 1.3 79.0 - - - +
558A LEU* 1.3 59.1 + - + +
560A ALA* 3.3 3.5 + - - +
561A LEU* 2.9 34.1 + - - +
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Residues in contact with LEU 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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543A LEU* 3.7 28.9 - - + -
551A GLN* 5.8 4.9 - - + +
554A PHE* 3.1 20.7 + - + +
555A ALA* 3.6 7.2 - - - +
557A ALA* 1.3 74.9 - - + +
559A GLU* 1.3 61.0 + - - +
561A LEU* 3.1 7.7 + - - +
562A ALA* 2.9 23.4 + - - +
568A TYR* 3.5 37.3 - - + +
570A LEU* 4.4 21.1 - - + -
623A ALA* 3.9 21.8 - - + -
91B TYR* 4.0 21.5 - - + +
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Residues in contact with GLU 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 ALA 2.9 15.2 + - - +
556A LEU* 3.9 6.3 - - + +
558A LEU* 1.3 76.5 - - - +
560A ALA* 1.3 57.6 + - - +
562A ALA* 3.1 2.8 + - - +
563A ARG* 2.9 45.2 + - + +
32B VAL* 3.4 20.9 - - + +
89B ARG* 2.8 37.4 + - - -
91B TYR* 2.3 49.6 + - + +
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Residues in contact with ALA 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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520A TRP* 3.6 39.2 - - + -
556A LEU* 2.9 18.2 + - + +
557A ALA 3.6 5.2 - - - +
559A GLU* 1.3 78.6 - - - +
561A LEU* 1.3 59.6 + - - +
563A ARG* 3.6 30.1 + - - +
564A GLU* 3.3 23.7 + - - +
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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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520A TRP* 5.1 0.7 - - + -
523A LEU* 3.8 21.1 - - + -
527A LEU* 4.1 15.9 - - + -
541A VAL* 3.6 26.7 - - + -
543A LEU* 3.7 23.1 - - + -
557A ALA 2.9 17.1 + - - +
558A LEU* 3.1 8.5 + - - +
560A ALA* 1.3 77.7 - - - +
562A ALA* 1.3 60.6 + - - +
564A GLU* 3.1 10.1 + - - +
566A ILE* 3.0 59.9 + - + +
568A TYR* 3.7 20.2 - - + -
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Residues in contact with ALA 562 (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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558A LEU 2.9 13.2 + - - +
559A GLU* 3.1 10.3 + - - +
561A LEU* 1.3 75.3 - - - +
563A ARG* 1.3 57.3 + - - +
565A GLY* 2.7 24.7 + - - +
566A ILE 4.2 5.4 + - - +
568A TYR* 4.2 9.2 - - + +
34B ASP* 5.3 4.3 - - - +
89B ARG* 3.4 40.8 - - - +
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Residues in contact with ARG 563 (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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520A TRP* 5.6 4.4 - - - +
556A LEU* 3.6 28.9 - - - +
559A GLU* 2.9 26.9 + - + +
560A ALA* 3.8 27.9 + - - +
562A ALA* 1.3 74.3 - - - +
564A GLU* 1.3 64.3 + - - +
565A GLY 3.5 0.5 + - - -
89B ARG* 5.4 0.2 - - - +
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Residues in contact with GLU 564 (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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520A TRP* 6.0 2.3 - - - -
527A LEU* 6.1 2.0 - - + -
531A ARG* 5.4 2.7 + - - -
537A LEU* 3.4 34.8 - - + +
560A ALA 3.3 12.2 + - - +
561A LEU 3.1 9.6 + - - +
562A ALA 3.0 0.8 - - - -
563A ARG* 1.3 83.3 - - - +
565A GLY* 1.3 58.1 + - - +
566A ILE* 3.1 19.6 + - + +
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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