Contacts of the helix formed by residues 548 - 563 (chain H) in PDB entry 5A31
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 LYS 548 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516H MET* 3.8 18.0 - - - +
519H GLU* 3.8 21.7 + - + +
543H LEU* 3.1 23.1 + - + +
546H LEU* 3.6 42.3 - - + +
547H GLN* 1.3 71.6 - - - +
549H ASP* 1.3 65.1 + - - +
550H VAL* 3.2 5.8 - - + -
551H ALA* 3.2 18.0 + - + +
552H LEU* 3.0 22.7 + - - +
579H LEU* 4.4 1.8 - - - -
151X GLN* 5.9 1.2 + - - -
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Residues in contact with ASP 549 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75E GLN* 4.7 10.5 - - - +
547H GLN 2.8 10.9 + - - +
548H LYS* 1.3 71.7 - - - +
550H VAL* 1.3 71.0 + - - +
552H LEU* 3.4 3.4 + - - +
553H SER* 3.0 29.6 + - - -
576H CYS* 4.8 0.9 - - - -
579H LEU* 3.6 20.6 - - + -
580H GLN* 3.5 34.1 + - - +
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Residues in contact with VAL 550 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71E LYS* 6.4 2.2 - - + -
75E GLN* 3.9 17.7 - - + +
78E ARG* 3.8 22.7 - - - +
548H LYS* 4.9 4.9 - - + -
549H ASP* 1.3 85.6 + - - +
551H ALA* 1.3 79.2 + - + +
553H SER* 3.1 15.1 + - - -
554H VAL* 3.3 12.2 + - + +
333Y ASN* 6.4 0.2 - - - +
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Residues in contact with ALA 551 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519H GLU* 6.1 1.3 - - - +
539H TYR* 5.5 3.0 + - - +
543H LEU* 4.0 12.7 - - + +
548H LYS* 3.2 25.1 + - + +
550H VAL* 1.3 86.2 - - + +
552H LEU* 1.3 63.5 + - - +
554H VAL* 3.2 12.0 + - - +
555H LEU* 3.2 19.4 + - - +
333Y ASN* 6.0 3.6 - - - +
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Residues in contact with LEU 552 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540H SER* 3.8 33.2 - - - +
543H LEU* 3.6 13.0 - - + +
544H TRP* 4.0 23.1 - - + +
548H LYS 3.0 15.2 + - - +
549H ASP 3.6 5.4 - - - +
551H ALA* 1.3 77.5 - - - +
553H SER* 1.3 57.3 + - - +
555H LEU* 3.1 15.3 + - + +
556H SER* 3.0 23.1 + - - +
572H ALA 4.2 7.0 - - - +
575H ASN* 4.1 5.8 - - + +
576H CYS* 3.3 34.3 - - - +
579H LEU* 3.8 24.9 - - + -
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Residues in contact with SER 553 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75E GLN* 3.2 23.0 + - - -
78E ARG* 3.4 17.2 - - - -
79E MET* 4.6 19.7 - - - -
82E LEU* 4.4 5.8 - - - +
549H ASP 3.0 11.3 + - - -
550H VAL 3.1 12.3 + - - -
552H LEU* 1.3 74.3 - - - +
554H VAL* 1.3 63.0 + - - +
556H SER* 4.1 0.6 - - - -
557H LYS* 3.0 26.9 + - - +
576H CYS* 3.3 15.0 - - - -
580H GLN* 6.1 0.2 - - - -
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Residues in contact with VAL 554 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78E ARG* 3.4 35.0 - - - +
526H ARG* 6.1 0.9 - - - +
550H VAL* 3.3 15.5 + - + +
551H ALA* 3.2 11.8 + - - +
553H SER* 1.3 77.4 + - - +
555H LEU* 1.3 65.8 - - - +
557H LYS* 3.6 2.8 + - - +
558H ASP* 3.0 27.7 + - + +
326Y ASN* 6.4 0.2 - - - +
329Y CYS* 5.5 5.6 - - + -
330Y ARG* 6.5 1.1 - - + -
333Y ASN* 5.0 14.6 - - - +
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Residues in contact with LEU 555 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526H ARG* 3.9 17.7 - - - +
536H MET* 4.3 8.3 - - + +
539H TYR* 3.8 36.6 - - + -
540H SER* 3.6 32.3 - - - +
543H LEU* 4.6 1.1 - - + -
551H ALA 3.2 7.6 + - - +
552H LEU* 3.1 19.4 + - + +
554H VAL* 1.3 81.2 - - - +
556H SER* 1.3 59.6 + - - +
558H ASP* 3.2 6.4 + - - +
559H LEU* 2.8 50.9 + - + +
572H ALA* 4.1 7.6 - - + -
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Residues in contact with SER 556 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82E LEU* 4.1 8.3 - - - -
552H LEU* 3.0 8.0 + - - +
553H SER 3.3 1.5 + - - -
554H VAL 3.3 0.2 - - - -
555H LEU* 1.3 74.5 - - - +
557H LYS* 1.3 63.7 + - - +
559H LEU* 3.3 2.5 + - - +
560H THR* 2.8 32.1 + - - +
572H ALA* 2.8 41.0 + - - +
573H ALA* 2.8 19.2 + - - +
576H CYS* 3.9 18.1 - - - -
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Residues in contact with LYS 557 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78E ARG* 4.2 31.1 - - + +
81E LYS* 4.2 26.9 - - + -
82E LEU* 4.0 17.5 - - + +
553H SER 3.0 16.6 + - - +
554H VAL* 4.1 3.1 - - - +
556H SER* 1.3 75.1 - - - +
558H ASP* 1.3 57.6 + - - +
560H THR* 3.4 4.6 + - - -
561H ASP* 2.9 60.9 + - - +
322Y GLU* 4.8 12.0 + - - +
325Y GLU* 5.7 5.1 + - - +
326Y ASN* 3.4 30.3 + - - +
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Residues in contact with ASP 558 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59F ARG* 4.3 13.6 + - - -
526H ARG* 3.1 30.3 + - - +
530H ASN* 6.0 0.7 - - - +
554H VAL* 3.0 25.2 + - + +
555H LEU 3.4 4.3 - - - +
557H LYS* 1.3 76.0 - - - +
559H LEU* 1.3 64.6 + - - +
561H ASP* 3.9 4.3 - - - +
562H MET* 3.1 22.3 + - - +
326Y ASN* 5.3 12.0 + - - +
330Y ARG* 5.4 7.2 + - - -
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Residues in contact with LEU 559 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526H ARG* 4.0 23.8 - - - +
532H ARG 4.9 1.6 - - - +
533H VAL* 3.7 30.3 - - + -
536H MET* 3.8 27.1 - - + -
555H LEU* 2.8 35.8 + - + +
556H SER* 4.0 3.6 - - - +
558H ASP* 1.3 73.2 - - - +
560H THR* 1.3 59.5 + - - +
562H MET* 3.3 13.3 + - + +
563H ASP* 2.8 32.9 + - - +
568H GLU 4.3 0.9 - - - +
569H ALA* 3.7 26.8 - - + +
572H ALA* 4.1 9.0 - - + -
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Residues in contact with THR 560 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82E LEU* 3.8 1.0 - - - +
85E LEU* 3.5 34.6 - - + +
556H SER 2.8 24.9 + - - +
557H LYS* 3.4 6.8 + - - -
559H LEU* 1.3 77.8 - - - +
561H ASP* 1.3 67.0 + - - +
563H ASP 2.9 21.1 + - - +
564H LYS* 4.2 17.6 + - - -
569H ALA* 4.0 23.6 - - + +
570H TRP* 4.4 19.5 - - + -
573H ALA* 4.3 10.8 - - + -
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Residues in contact with ASP 561 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81E LYS* 4.2 16.8 + - - -
82E LEU* 5.9 0.2 - - - +
85E LEU* 5.7 1.4 - - - +
557H LYS* 2.9 50.4 + - - +
558H ASP* 3.9 5.7 - - - +
560H THR* 1.3 82.7 + - - +
562H MET* 1.3 63.1 + - - +
563H ASP 3.4 0.2 + - - -
564H LYS* 5.8 1.3 - - - +
322Y GLU* 4.6 7.4 - - - +
326Y ASN* 5.9 0.2 + - - -
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Residues in contact with MET 562 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F TYR* 3.2 44.2 - - + +
59F ARG* 3.4 47.6 + - - +
526H ARG* 4.6 1.8 - - - -
530H ASN 4.2 7.9 - - - +
531H TYR 2.7 32.3 - - - +
532H ARG 4.5 0.4 - - - -
533H VAL* 3.8 22.0 - - + -
558H ASP* 3.1 15.5 + - - +
559H LEU* 3.6 19.1 - - + +
561H ASP* 1.3 79.2 - - - +
563H ASP* 1.3 59.9 + - + +
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Residues in contact with ASP 563 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55F TYR* 2.9 41.3 + - + -
533H VAL* 5.3 2.0 - - + -
559H LEU 2.8 24.1 + - - +
560H THR* 2.9 18.4 - - - +
561H ASP 3.2 2.4 - - - -
562H MET* 1.3 88.5 - - + +
564H LYS* 1.3 80.3 + - - +
565H ASN* 4.7 0.9 - - - +
566H SER* 2.7 31.5 + - - -
569H ALA* 3.9 4.9 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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