Contacts of the helix formed by residues 441 - 451 (chain B) in PDB entry 2R5N
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 441 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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411B GLU* 3.4 33.2 - - + +
412B PHE* 3.8 12.1 - - - +
414B MET* 6.0 0.2 - - + -
415B THR* 3.4 15.3 - - - +
433B THR* 6.2 0.9 - - + -
437B PHE 3.6 2.6 + - - +
438B VAL* 3.0 10.3 + - - +
440B TYR* 1.3 76.3 - - - +
442B ARG* 1.3 65.5 + - - +
443B ASN 3.3 2.5 - - - -
444B ALA* 2.9 16.9 + - - +
445B VAL* 3.1 15.2 + - + +
459B TYR* 5.2 2.0 - - + +
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Residues in contact with ARG 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A GLU* 3.7 39.5 + - + +
442A ARG* 4.7 9.6 - - + -
477A GLU* 5.0 3.6 + - - +
438B VAL* 2.8 30.0 + - - +
439B GLU* 3.6 17.2 + - - +
440B TYR 3.4 3.4 + - - -
441B ALA* 1.3 76.8 - - - +
443B ASN* 1.3 63.1 + - - +
445B VAL* 3.3 19.0 + - - +
446B ARG* 3.1 27.6 + - - +
478B GLN 5.5 0.2 + - - -
481B SER* 3.0 39.5 + - - -
482B LEU* 3.7 13.9 - - - +
485B THR* 2.7 30.7 + - - +
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Residues in contact with ASN 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436A MET* 3.9 23.9 + - - +
437A PHE* 4.8 0.5 - - - -
439A GLU* 2.8 35.5 + - + +
440A TYR* 3.6 30.0 - - + +
472A THR 5.2 0.6 + - - -
115B PRO* 3.5 19.1 - - - +
118B GLN* 2.9 23.7 + - - +
412B PHE* 4.5 3.7 - - + -
441B ALA 3.3 0.8 - - - -
442B ARG* 1.3 79.1 - - - +
444B ALA* 1.3 56.6 + - - +
446B ARG* 3.3 8.0 + - - +
447B MET* 2.9 30.9 + - - +
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Residues in contact with ALA 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B GLN* 3.3 14.8 - - - +
412B PHE* 3.6 25.1 - - + -
415B THR* 3.7 19.4 - - + +
416B ALA* 3.8 17.3 - - + +
419B ASN* 3.0 12.6 + - - +
441B ALA 2.9 9.2 + - - +
443B ASN* 1.3 75.0 - - - +
445B VAL* 1.3 60.7 + - - +
447B MET* 3.3 0.6 + - - -
448B ALA* 3.0 24.9 + - - +
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Residues in contact with VAL 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B THR* 4.0 10.3 - - + -
438B VAL* 3.8 13.0 - - + -
441B ALA* 3.1 14.9 + - + +
442B ARG* 3.5 15.7 - - - +
443B ASN 3.3 0.2 - - - -
444B ALA* 1.3 74.9 - - - +
446B ARG* 1.3 65.1 + - - +
448B ALA* 3.2 13.3 + - - +
449B ALA 3.2 8.8 + - - -
457B MET* 4.0 16.8 - - - -
459B TYR* 3.4 25.1 - - + +
482B LEU* 3.9 19.1 - - + -
488B MET* 3.4 30.8 - - + +
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Residues in contact with ARG 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A MET* 3.3 16.9 - - - +
439A GLU* 3.6 24.2 - - - +
471A PRO 3.0 24.5 + - - -
472A THR* 4.6 4.0 + - - +
474A GLN 3.6 17.0 + - - -
476A VAL* 4.0 7.7 - - - +
477A GLU* 2.8 39.6 + - - +
478A GLN* 3.3 8.1 - - - +
635A PHE* 3.3 35.5 - - + +
442B ARG* 3.1 14.6 + - - +
443B ASN* 3.5 16.8 - - - +
444B ALA 3.3 0.2 - - - -
445B VAL* 1.3 78.2 - - - +
447B MET* 1.3 60.7 + - + +
449B ALA* 3.0 8.1 + - - +
450B LEU* 2.8 32.2 + - + +
485B THR* 4.6 4.3 - - + -
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Residues in contact with MET 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472A THR* 4.2 7.0 - - + +
112B THR* 3.2 50.7 - - + +
115B PRO* 3.8 19.1 - - + -
118B GLN* 3.4 23.1 - - + +
419B ASN* 4.0 6.1 - - - +
443B ASN* 2.9 28.9 + - - +
444B ALA 3.7 5.8 - - - +
445B VAL 3.2 0.2 - - - -
446B ARG* 1.3 79.5 - - - +
448B ALA* 1.3 60.2 + - - +
450B LEU* 4.0 19.5 - - + -
451B MET* 2.9 49.3 + - + +
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Residues in contact with ALA 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419B ASN* 3.3 25.0 - - - +
444B ALA 3.0 10.3 + - - +
445B VAL 3.2 10.1 + - - +
447B MET* 1.3 74.8 - - - +
449B ALA* 1.3 63.1 + - - +
451B MET 3.5 0.5 + - - -
452B LYS 3.1 3.5 + - - -
453B GLN* 3.0 38.5 + - + -
455B GLN* 4.4 2.2 - - + +
457B MET* 3.8 20.2 - - + -
513B PRO* 3.9 12.4 - - + +
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Residues in contact with ALA 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635A PHE* 3.9 5.6 - - + -
445B VAL 3.2 8.3 + - - +
446B ARG 3.0 9.4 + - - +
448B ALA* 1.3 81.0 - - - +
450B LEU* 1.3 62.2 + - - +
452B LYS 3.1 4.2 + - - -
485B THR* 4.3 8.1 - - + -
486B PRO 3.3 23.8 - - - +
487B ASN* 3.0 32.8 + - - +
488B MET* 4.2 3.1 - - + +
513B PRO* 3.7 16.3 - - + +
679B EDO 3.2 5.4 - - - -
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Residues in contact with LEU 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471A PRO* 4.2 16.6 - - + +
472A THR* 3.9 38.6 - - + +
635A PHE* 3.5 43.0 - - + -
102B GLU* 6.0 2.5 - - + +
112B THR* 4.4 7.9 - - + +
446B ARG* 2.8 23.7 + - + +
447B MET* 3.4 22.0 + - + +
449B ALA* 1.3 71.7 - - - +
451B MET* 1.3 59.3 + - - +
452B LYS* 3.3 5.7 + - - +
679B EDO 2.8 22.9 + - - +
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Residues in contact with MET 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B VAL* 3.9 21.6 - - + +
111B THR* 3.5 12.8 - - - +
112B THR* 3.4 49.8 - - + +
122B ASN* 4.7 4.5 - - - +
419B ASN* 4.0 33.4 - - + +
423B LEU* 4.0 10.3 - - + -
447B MET* 2.9 37.4 + - + +
450B LEU* 1.3 74.1 - - + +
452B LYS* 1.3 69.7 + - - +
453B GLN* 3.0 24.3 - - + +
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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