Contacts of the strand formed by residues 486 - 494 (chain J) in PDB entry 2ONM
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 486 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139J TYR* 3.7 16.1 - - + +
156J HIS* 3.4 33.2 - - + +
157J GLU 3.3 8.6 + - - +
159J VAL* 4.4 1.8 - - - +
185J THR* 3.9 12.0 - - - +
264J ARG* 2.7 27.7 + - - +
482J LEU 3.3 14.8 + - - -
483J GLN* 3.3 8.6 + - - +
484J ALA 3.4 1.8 + - - -
485J TYR* 1.3 81.5 + - - +
487J LYS* 1.3 77.5 + - - +
488J VAL* 4.6 6.6 - - + +
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Residues in contact with LYS 487 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447I GLN* 6.3 0.2 - - - +
468I TYR* 4.0 57.4 - - + +
469I LYS* 5.0 7.6 - - - +
475I ARG* 4.7 4.9 - - - +
70J PHE* 6.0 2.2 - - - -
155J ARG 3.3 2.6 - - - +
157J GLU* 2.7 39.5 + - + +
158J PRO 3.8 10.2 + - - +
159J VAL* 3.4 42.4 + - + +
239J ASP* 5.2 7.1 - - - -
264J ARG* 4.9 7.2 - - - +
486J THR* 1.3 77.3 - - - +
488J VAL* 1.3 62.6 + - - +
489J LYS 3.7 0.3 + - - -
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Residues in contact with VAL 488 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449I GLY 3.8 5.2 - - - +
464I PRO* 4.1 10.8 - - + -
468I TYR* 4.0 2.3 - - - -
475I ARG* 3.1 44.7 + - + +
480I TYR* 3.6 49.6 - - + -
483I GLN* 5.8 1.6 - - - +
154J THR* 3.9 19.7 - - + -
155J ARG 3.6 3.4 - - - +
156J HIS* 4.4 9.0 - - + -
486J THR* 4.3 7.2 + - + +
487J LYS* 1.3 75.8 - - - +
489J LYS* 1.3 60.7 + - - +
490J THR* 4.1 0.7 + - - -
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Residues in contact with LYS 489 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443I SER 3.0 20.2 + - - +
444I GLN* 3.0 23.6 + - - +
446I LEU 2.7 29.4 + - - -
447I GLN* 5.0 0.2 - - - +
448I ALA 3.4 19.5 - - - +
449I GLY 3.7 3.6 - - - -
451I VAL* 4.3 4.5 - - + -
468I TYR* 3.1 23.1 - - - +
153J TYR 3.9 0.2 - - - +
154J THR* 3.1 5.0 - - - -
155J ARG* 2.7 49.7 + - + +
157J GLU* 3.1 25.7 + - - +
487J LYS 3.7 1.0 + - - -
488J VAL* 1.3 73.7 - - - +
490J THR* 1.3 70.8 + - - +
491J VAL* 4.1 11.0 + - + +
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Residues in contact with THR 490 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449I GLY 2.9 13.0 + - - -
450I THR* 3.3 10.6 - - + +
451I VAL 2.9 25.5 + - - -
463I SER* 4.2 12.1 - - - +
464I PRO* 2.9 46.6 + - + +
475I ARG* 6.0 0.3 - - - -
152J SER* 3.8 12.1 - - - +
153J TYR 3.4 7.6 - - - +
154J THR* 3.8 1.9 - - + +
488J VAL* 4.7 1.4 + - - +
489J LYS* 1.3 74.2 - - - +
491J VAL* 1.3 64.4 + - - +
492J THR* 3.8 18.2 - - - +
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Residues in contact with VAL 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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443I SER* 4.0 24.9 - - - +
451I VAL* 3.4 13.9 - - + +
453I VAL* 4.4 2.9 - - + -
151J PHE 3.5 0.5 - - - +
152J SER* 3.3 2.5 - - - -
153J TYR* 2.8 81.5 + - + +
155J ARG* 4.9 4.5 - - - -
489J LYS* 4.1 22.7 - - + +
490J THR* 1.3 77.3 - - - +
492J THR* 1.3 61.6 + - - +
493J VAL* 3.8 15.5 - - + -
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Residues in contact with THR 492 (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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450I THR* 4.9 1.9 - - - +
451I VAL 3.1 6.3 + - - -
452I TRP* 3.4 22.4 + - + -
453I VAL 3.1 22.5 + - - -
455I CYS* 3.7 4.2 - - - -
458I VAL* 4.0 26.2 + - + +
463I SER* 4.6 2.4 + - - -
146J ILE* 4.4 5.4 - - + +
150J PHE* 3.9 25.6 - - + -
151J PHE 3.4 2.9 - - - -
152J SER* 3.0 24.0 + - - +
490J THR* 3.8 10.3 - - - +
491J VAL* 1.3 71.4 - - - +
493J VAL* 1.3 61.6 + - - +
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Residues in contact with VAL 493 (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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453I VAL* 3.8 31.2 - - + +
150J PHE* 3.1 8.0 - - - -
151J PHE* 2.7 54.9 + - + +
153J TYR* 4.5 9.0 - - + +
491J VAL* 3.8 22.0 - - + -
492J THR* 1.3 75.6 - - - +
494J LYS* 1.3 74.1 + - - +
495J VAL* 3.5 0.9 + - + +
436L LEU* 4.2 11.4 - - + -
440L ASN* 4.0 18.2 - - - +
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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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285I TRP* 3.7 34.7 - - + +
453I VAL 3.2 12.1 + - - +
454I ASN* 3.3 37.8 + - + +
455I CYS* 4.3 1.3 - - + -
149J ASP* 4.3 5.2 - - + +
150J PHE* 3.6 22.1 - - + -
493J VAL* 1.3 81.0 - - - +
495J VAL* 1.3 73.3 + - - +
496J PRO* 5.7 2.4 + - - +
437L ASP* 4.0 18.7 - - - +
440L ASN* 4.9 1.2 + - - -
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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