Contacts of the helix formed by residues 487 - 506 (chain J) in PDB entry 4XLN
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 ALA 487 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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485J SER* 3.1 7.9 + - - +
486J ARG* 1.3 77.5 - - - +
488J ARG* 1.3 60.8 + - - +
490J ALA* 2.9 30.2 + - - +
491J LYS* 3.4 7.1 + - - +
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Residues in contact with ARG 488 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480J GLU* 3.2 38.7 + - - +
483J HIS* 3.1 47.0 + - + -
485J SER* 3.5 20.1 + - - +
487J ALA* 1.3 78.0 - - - +
489J ARG* 1.3 56.9 + - - +
491J LYS* 3.6 4.8 + - - +
492J ALA* 2.9 32.8 + - - +
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Residues in contact with ARG 489 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480J GLU 4.7 0.4 + - - -
481J MET* 3.3 40.4 + - + +
482J LYS 5.1 1.8 + - - -
483J HIS 3.5 10.4 + - - +
484J PRO* 3.3 35.5 + - - +
485J SER 3.2 13.9 + - - +
486J ARG* 3.3 36.0 - - - +
488J ARG* 1.3 77.5 - - - +
490J ALA* 1.3 61.0 + - + +
492J ALA* 4.3 4.0 - - - -
493J ARG* 2.9 23.0 + - - +
1391J GLU* 3.6 29.9 + - - +
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Residues in contact with ALA 490 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486J ARG 4.1 8.5 - - - +
487J ALA* 2.9 13.3 + - - +
489J ARG* 1.3 79.0 - - + +
491J LYS* 1.3 60.6 + - - +
493J ARG* 3.0 30.0 + - - +
494J LYS* 2.9 38.3 + - - +
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Residues in contact with LYS 491 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117J ASP* 4.1 22.4 + - - -
487J ALA 3.4 6.9 + - - +
488J ARG* 4.2 6.1 - - - +
490J ALA* 1.3 78.0 - - - +
492J ALA* 1.3 61.9 + - - +
494J LYS* 3.3 10.8 + - + +
495J ARG* 2.9 27.2 + - + +
46R T 6.0 0.6 + - - -
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Residues in contact with ALA 492 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477J LEU* 4.3 18.1 - - + +
480J GLU* 3.8 20.2 + - + +
481J MET* 4.2 24.5 - - - +
488J ARG 2.9 21.0 + - - +
489J ARG 3.8 4.9 - - - +
491J LYS* 1.3 77.3 - - - +
493J ARG* 1.3 62.4 + - - +
495J ARG* 3.9 1.7 - - - +
496J LEU* 2.9 27.2 + - - +
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Residues in contact with ARG 493 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481J MET* 3.6 21.7 - - + -
489J ARG 2.9 16.3 + - - +
490J ALA* 3.1 25.5 + - - +
492J ALA* 1.3 74.6 - - - +
494J LYS* 1.3 93.0 + - - +
496J LEU* 3.0 4.7 + - - +
497J GLU* 2.9 43.9 + - - +
1390J LEU* 5.3 4.0 - - + -
1391J GLU 3.6 20.9 + - - +
1392J GLY* 4.1 27.0 + - - -
1393J GLN* 5.1 1.8 - - - +
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Residues in contact with LYS 494 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114J THR* 3.8 8.8 - - + +
490J ALA* 2.9 26.4 + - - +
491J LYS* 3.3 9.6 + - + +
493J ARG* 1.3 108.3 - - - +
495J ARG* 1.3 59.7 + - - +
497J GLU* 3.5 20.9 - - - +
498J VAL* 3.6 13.7 - - - +
45R A 4.7 21.8 - - - +
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Residues in contact with ARG 495 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114J THR* 3.2 29.3 + - + +
115J LEU* 3.0 25.7 + - - +
117J ASP* 3.7 27.0 + - - +
150J ARG* 3.4 25.3 - - - +
473J LEU* 3.7 34.5 - - - +
476J GLU* 5.7 1.6 + - - -
477J LEU* 3.6 23.6 - - + +
491J LYS* 2.9 20.3 + - + +
492J ALA* 3.9 4.3 - - - +
494J LYS* 1.3 72.8 - - - +
496J LEU* 1.3 64.0 + - - +
497J GLU 3.0 4.5 - - - -
498J VAL* 3.0 7.4 + - - +
499J VAL* 3.0 26.6 + - + +
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Residues in contact with LEU 496 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474J GLU* 3.7 42.6 - - + +
477J LEU* 3.7 22.3 - - + +
478J LEU* 3.7 24.5 - - + -
481J MET* 3.7 25.1 - - + -
492J ALA 2.9 18.9 + - - +
493J ARG 3.5 3.8 - - - +
495J ARG* 1.3 75.5 - - - +
497J GLU* 1.3 56.1 + - - +
499J VAL* 3.8 6.1 - - + -
500J ARG* 2.9 46.1 + - + +
1390J LEU* 3.9 13.9 - - + -
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Residues in contact with GLU 497 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493J ARG* 2.9 34.7 + - - +
494J LYS* 3.5 17.3 - - - +
495J ARG 3.0 0.4 - - - -
496J LEU* 1.3 75.1 - - - +
498J VAL* 1.3 61.2 + - + +
500J ARG* 3.5 6.2 + - - +
501J ALA* 2.9 26.9 + - - +
1393J GLN* 5.3 23.7 - - + +
1394J VAL 5.9 0.5 + - - -
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Residues in contact with VAL 498 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111J LYS* 4.0 42.4 - - + +
114J THR* 3.8 22.9 - - + -
115J LEU* 3.6 20.0 - - + -
494J LYS 3.6 16.6 - - - +
495J ARG 3.0 4.0 + - - +
497J GLU* 1.3 73.2 - - + +
499J VAL* 1.3 67.9 + - - +
501J ALA* 3.0 7.7 + - - +
502J PHE* 3.0 43.6 + - + -
1452J ILE* 4.6 3.8 - - + -
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Residues in contact with VAL 499 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115J LEU* 3.7 20.4 - - + -
470J LEU* 3.4 38.7 - - + +
473J LEU* 3.7 22.4 - - + -
474J GLU* 4.3 11.7 - - + +
477J LEU* 4.0 11.4 - - + -
495J ARG* 3.0 16.7 + - + +
496J LEU* 3.7 10.3 - - + +
498J VAL* 1.3 75.2 - - - +
500J ARG* 1.3 56.3 - - - +
502J PHE* 3.2 5.2 + - - +
503J LEU* 2.9 34.4 + - + +
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Residues in contact with ARG 500 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474J GLU* 3.0 34.9 + - - +
478J LEU* 3.7 31.7 - - - +
496J LEU* 2.9 33.9 + - + +
497J GLU* 3.7 6.1 - - - +
499J VAL* 1.3 73.5 - - - +
501J ALA* 1.3 60.7 + - - +
503J LEU* 4.2 10.8 - - - -
504J ASP* 2.9 49.3 + - - +
1388J ARG* 3.6 20.3 + - - +
1390J LEU* 3.4 31.1 - - + +
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Residues in contact with ALA 501 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497J GLU 2.9 15.4 + - - +
498J VAL* 3.0 12.1 + - - +
500J ARG* 1.3 76.7 - - - +
502J PHE* 1.3 57.6 + - - +
504J ASP* 4.1 3.0 - - - +
505J SER* 2.9 33.4 + - - -
1449J GLU 5.7 0.2 - - - +
1452J ILE* 3.5 24.4 - - + +
1453J ALA* 4.0 19.9 - - + +
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Residues in contact with PHE 502 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12J LEU* 4.3 8.7 - - + -
111J LYS* 5.3 0.7 - - + -
115J LEU* 4.1 15.5 - - + -
470J LEU* 4.6 14.8 - - + -
498J VAL* 3.0 44.5 + - + -
499J VAL 3.6 6.7 - - - +
501J ALA* 1.3 78.3 - - - +
503J LEU* 1.3 61.4 + - - +
505J SER* 3.0 6.5 + - - -
506J GLY* 3.0 19.6 + - - -
507J ASN* 3.3 30.2 + - + +
508J ARG 4.2 2.5 - - - -
509J PRO* 3.5 30.3 - - + -
512J MET* 3.4 31.0 - - + -
1452J ILE* 3.5 28.3 - - + -
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Residues in contact with LEU 503 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470J LEU* 3.6 44.2 - - + +
471J GLU* 4.4 13.0 - - + +
474J GLU* 3.8 31.6 - - + +
499J VAL* 2.9 22.1 + - + +
500J ARG* 3.8 11.9 - - - +
501J ALA 3.3 0.2 - - - -
502J PHE* 1.3 77.6 - - - +
504J ASP* 1.3 66.0 + - - +
506J GLY* 3.5 8.8 + - - -
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Residues in contact with ASP 504 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9J ARG* 5.3 3.6 + - - -
500J ARG* 2.9 34.9 + - - +
501J ALA* 4.1 3.6 - - - +
503J LEU* 1.3 78.6 - - - +
505J SER* 1.3 66.3 + - - +
506J GLY 3.4 0.5 + - - -
1453J ALA 4.8 4.0 - - - +
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Residues in contact with SER 505 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9J ARG* 4.4 19.3 + - - +
501J ALA 2.9 22.2 + - - -
502J PHE* 3.0 12.8 + - - -
504J ASP* 1.3 78.1 - - - +
506J GLY* 1.3 60.7 + - - +
507J ASN* 3.2 29.9 + - - +
1452J ILE 3.1 20.0 + - - -
1453J ALA 3.3 17.6 + - - -
1454J GLY* 3.9 3.1 - - - -
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Residues in contact with GLY 506 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502J PHE 3.0 9.1 + - - -
503J LEU* 3.5 7.6 + - - -
504J ASP 3.2 3.4 - - - -
505J SER* 1.3 78.1 - - - +
507J ASN* 1.3 63.4 + - - +
508J ARG* 4.1 3.9 + - - +
511J TRP* 4.9 4.2 - - - -
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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