Contacts of the helix formed by residues 410 - 425 (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 ARG 410 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A MET* 3.9 21.4 + - + +
196A TRP 2.8 30.9 + - - -
197A PHE* 3.8 16.8 - - - +
165B GLU* 3.2 52.5 + - + +
168B SER* 3.0 27.6 + - - -
169B LEU* 3.9 19.6 - - - +
380B ALA* 4.1 3.4 - - - +
407B TYR* 2.9 35.2 + - + +
408B GLY* 2.9 12.5 + - - -
409B VAL* 1.3 79.8 - - - +
411B GLU* 1.3 59.6 + - - +
413B GLY* 4.9 0.2 - - - -
414B MET* 2.8 32.2 + - - +
417B ILE* 6.3 0.7 - - - -
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Residues in contact with GLU 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A GLU* 2.6 28.6 - - - +
672A TPP 2.7 37.3 + - - -
165B GLU* 3.7 0.8 + - - -
380B ALA* 4.1 8.7 - - + +
409B VAL* 3.9 5.0 - - - +
410B ARG* 1.3 75.6 - - - +
412B PHE* 1.3 61.1 + - - +
414B MET* 3.6 10.1 - - + +
415B THR* 2.8 31.4 + - - -
433B THR* 3.7 33.3 + - + +
437B PHE* 3.8 21.3 - - + +
440B TYR* 3.5 11.5 - - + +
441B ALA* 3.4 6.0 - - + +
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Residues in contact with PHE 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A GLU* 5.7 0.2 + - - -
440A TYR* 3.6 56.3 - + + -
118B GLN* 3.8 9.4 - - - -
160B GLU* 5.5 0.2 - - - -
162B ILE* 3.7 35.2 - - + -
165B GLU* 3.5 12.7 + - - +
410B ARG 3.3 0.4 - - - -
411B GLU* 1.3 76.6 + - - +
413B GLY* 1.3 65.2 + - - +
415B THR* 3.2 3.6 + - - -
416B ALA* 3.0 20.6 + - - +
440B TYR* 3.4 21.2 + - + +
441B ALA* 3.8 13.6 - - - +
443B ASN* 4.5 3.1 - - + -
444B ALA* 3.6 34.1 - - + -
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Residues in contact with GLY 413 (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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162B ILE* 3.8 10.4 - - - +
165B GLU* 2.7 25.1 + - - -
166B VAL* 3.5 24.1 - - - +
410B ARG* 4.0 0.9 - - - -
412B PHE* 1.3 72.2 - - - +
414B MET* 1.3 51.7 + - - +
417B ILE* 2.7 43.9 + - - +
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Residues in contact with MET 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B SER 4.1 0.2 - - - -
380B ALA* 3.7 20.4 - - + -
407B TYR* 3.5 51.8 - - + -
410B ARG* 2.8 25.0 + - - +
411B GLU* 3.6 15.5 - - + +
413B GLY* 1.3 72.3 - - - +
415B THR* 1.3 62.3 + - - +
417B ILE* 3.6 2.3 - - - +
418B ALA* 2.9 27.7 + - - +
431B THR* 3.7 17.0 - - + +
432B SER* 3.3 46.2 - - - +
433B THR* 4.4 8.1 - - + -
459B TYR* 5.7 2.0 - - + -
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Residues in contact with THR 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B GLU 2.8 17.6 + - - -
412B PHE 3.8 0.9 - - - -
414B MET* 1.3 87.1 - - - +
416B ALA* 1.3 57.9 + - - +
418B ALA* 3.3 3.5 + - - +
419B ASN* 3.0 27.0 + - - +
431B THR* 4.5 3.5 + - - +
441B ALA* 3.4 10.8 - - - +
444B ALA* 3.7 33.4 - - + +
445B VAL* 3.9 15.9 - - + +
455B GLN* 3.7 20.4 + - - +
457B MET* 4.2 7.4 - - + -
459B TYR* 4.7 5.9 + - - +
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Residues in contact with ALA 416 (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* 4.3 8.3 - - + +
121B ALA* 3.4 25.4 - - + -
122B ASN* 3.0 29.5 + - - +
162B ILE* 3.7 10.5 - - + -
412B PHE 3.0 15.0 + - - +
413B GLY 4.1 0.2 - - - +
415B THR* 1.3 74.1 - - - +
417B ILE* 1.3 65.8 + - - +
419B ASN* 3.2 10.0 + - - +
420B GLY 3.1 9.0 + - - -
444B ALA* 3.8 10.4 - - + +
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Residues in contact with ILE 417 (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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121B ALA 3.6 19.5 + - - +
124B VAL* 3.8 17.9 - - + -
125B GLY* 3.3 16.0 - - - -
128B ILE* 3.8 15.0 - - + -
165B GLU 5.5 0.7 - - - +
166B VAL* 3.7 23.3 - - + -
169B LEU* 3.8 25.8 - - + -
407B TYR* 3.9 15.9 - - + -
410B ARG* 6.3 0.7 - - - -
413B GLY 2.7 30.4 + - - +
414B MET 3.6 3.6 - - - +
416B ALA* 1.3 72.3 - - - +
418B ALA* 1.3 57.0 + - - +
420B GLY* 2.9 18.7 + - - -
421B ILE* 2.9 19.6 + - + +
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Residues in contact with ALA 418 (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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407B TYR* 4.3 3.3 + - - +
414B MET 2.9 7.7 + - - +
415B THR 3.5 4.3 - - - +
416B ALA 3.3 0.2 - - - -
417B ILE* 1.3 76.7 - - - +
419B ASN* 1.3 57.0 + - - +
421B ILE* 3.1 14.0 + - - +
422B SER* 2.9 27.4 + - - -
429B PRO* 3.6 15.1 - - + +
431B THR* 3.4 32.5 - - + -
455B GLN* 3.5 19.7 - - - +
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Residues in contact with ASN 419 (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* 4.6 2.2 + - - -
122B ASN* 3.8 9.3 - - - +
415B THR* 3.0 15.5 + - - +
416B ALA* 3.3 14.4 - - - +
417B ILE 3.2 0.2 - - - -
418B ALA* 1.3 76.0 - - - +
420B GLY* 1.3 56.2 + - - +
422B SER* 2.8 21.8 + - - -
423B LEU* 3.0 23.4 + - - +
444B ALA* 3.0 27.1 + - - +
447B MET* 4.0 9.7 - - - +
448B ALA* 3.3 22.3 - - - +
451B MET* 4.0 15.9 - - + +
453B GLN* 5.0 1.7 - - + +
455B GLN* 3.0 21.0 + - - -
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Residues in contact with GLY 420 (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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122B ASN* 3.3 33.0 - - - +
125B GLY 3.9 6.1 - - - -
126B MET* 3.5 8.9 - - - +
416B ALA 3.1 6.9 + - - -
417B ILE 2.9 7.3 + - - -
419B ASN* 1.3 72.9 - - - +
421B ILE* 1.3 60.4 + - - +
423B LEU* 3.3 4.0 + - - +
424B HIS* 3.0 30.0 + - - +
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Residues in contact with ILE 421 (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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125B GLY* 3.6 20.8 - - - +
128B ILE* 4.5 4.0 - - + -
129B ALA* 4.5 4.6 - - + +
376B LEU* 3.9 28.5 - - + +
405B ILE* 3.9 9.9 - - + -
407B TYR* 3.7 23.6 - - - +
417B ILE* 2.9 22.3 + - + +
418B ALA* 3.1 10.3 + - - +
420B GLY* 1.3 75.5 - - - +
422B SER* 1.3 63.1 + - - +
424B HIS* 3.3 14.9 + - - +
425B GLY* 3.7 6.4 + - - +
427B PHE* 3.6 34.1 - - + +
429B PRO* 4.0 17.0 - - + -
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Residues in contact with SER 422 (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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418B ALA 2.9 13.7 + - - -
419B ASN* 2.8 18.7 + - - -
421B ILE* 1.3 76.9 - - - +
423B LEU* 1.3 60.0 + - - +
424B HIS 3.3 0.7 + - - -
425B GLY* 3.4 11.8 + - - -
427B PHE 4.9 5.1 - - - +
429B PRO* 4.0 10.3 - - - +
453B GLN* 2.8 38.3 + - - +
454B ARG* 3.5 26.0 - - - -
455B GLN* 5.4 1.5 + - - -
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Residues in contact with LEU 423 (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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57B ARG* 4.8 8.8 + - - -
103B VAL* 4.0 24.2 - - + -
110B GLU* 3.5 20.3 - - - +
111B THR* 3.3 33.0 - - - +
122B ASN* 4.6 2.5 - - - +
126B MET* 4.1 12.1 - - + -
419B ASN 3.0 30.5 + - - +
420B GLY* 3.7 5.2 - - - +
422B SER* 1.3 77.5 + - - +
424B HIS* 1.3 63.7 + - - +
425B GLY 3.4 0.3 + - - -
451B MET* 4.0 11.2 - - + -
453B GLN* 3.5 30.3 - - + +
674B EDO 5.8 0.3 + - - -
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Residues in contact with HIS 424 (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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57B ARG* 5.0 1.0 + - - -
59B ARG* 2.9 55.7 + - - +
126B MET* 3.5 29.2 - - + -
129B ALA* 3.5 20.6 - - + +
130B GLU* 4.0 8.2 + - - -
133B LEU* 4.1 19.3 - - + +
147B HIS* 2.8 36.0 + + - -
329B MET* 3.6 7.4 - - + +
420B GLY 3.0 17.0 + - - +
421B ILE 3.5 7.0 - - - +
422B SER 3.2 0.6 - - - -
423B LEU* 1.3 80.5 - - - +
425B GLY* 1.3 76.2 + - - +
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Residues in contact with GLY 425 (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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133B LEU* 4.5 0.5 - - - +
329B MET* 3.7 23.6 - - - +
421B ILE 3.7 2.5 + - - -
422B SER 3.4 10.4 + - - -
423B LEU 3.3 4.0 - - - -
424B HIS* 1.3 98.3 + - - +
426B GLY* 1.3 57.9 + - - -
427B PHE* 3.4 13.6 + - - -
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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