Contacts of the helix formed by residues 410 - 425 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A GLU* 3.3 52.9 + - + +
168A SER* 2.9 27.3 + - - -
169A LEU* 3.9 21.2 - - - +
172A THR* 5.0 0.2 + - - -
380A ALA* 4.0 3.8 - - - +
407A TYR* 2.9 34.9 + - + +
408A GLY* 2.9 12.9 + - - -
409A VAL* 1.3 80.1 - - - +
411A GLU* 1.3 60.8 + - - +
413A GLY* 4.9 0.4 - - - -
414A MET* 2.8 32.2 + - + +
159B MET* 4.0 21.8 + - + +
196B TRP 2.7 29.3 + - - -
197B PHE* 3.8 17.6 - - - +
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Residues in contact with GLU 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A GLU* 3.8 1.2 + - - -
380A ALA* 4.1 9.0 - - + +
409A VAL* 3.9 4.9 - - - +
410A ARG* 1.3 76.7 - - - +
412A PHE* 1.3 61.3 + - - +
414A MET* 3.5 12.6 - - + +
415A THR* 2.9 30.8 + - - -
433A THR* 3.7 27.3 + - + +
437A PHE* 3.8 24.7 - - + +
440A TYR* 3.6 11.9 - - + +
441A ALA* 3.6 5.8 - - + -
160B GLU* 2.5 28.2 - - - +
672B TPP 2.7 36.9 + - - -
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Residues in contact with PHE 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A GLN* 3.7 17.0 - - + -
162A ILE* 3.8 28.3 - - + -
165A GLU* 3.5 11.8 + - - +
410A ARG 3.4 0.6 - - - -
411A GLU* 1.3 75.8 + - - +
413A GLY* 1.3 66.8 + - - +
415A THR* 3.1 2.9 + - - -
416A ALA* 3.0 21.1 + - - +
440A TYR* 3.3 22.8 - - + +
441A ALA* 3.7 15.2 - - - +
443A ASN* 4.5 2.7 - - + -
444A ALA* 3.6 34.8 - - + -
440B TYR* 3.6 56.1 - + + -
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Residues in contact with GLY 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A ILE* 3.8 8.4 - - - +
165A GLU* 2.7 25.4 + - - -
166A VAL* 3.5 26.3 - - - +
410A ARG* 4.9 1.3 - - - -
412A PHE* 1.3 74.1 - - - +
414A MET* 1.3 52.0 + - - +
416A ALA 3.4 0.3 + - - -
417A ILE* 2.7 43.1 + - - +
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Residues in contact with MET 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379A SER 4.1 0.4 - - - -
380A ALA* 3.7 20.6 - - + -
407A TYR* 3.5 52.4 - - + -
410A ARG* 2.8 23.8 + - - +
411A GLU* 3.5 15.7 - - + +
413A GLY* 1.3 72.1 - - - +
415A THR* 1.3 63.6 + - - +
417A ILE* 3.6 1.9 - - - +
418A ALA* 2.9 27.0 + - - +
431A THR* 3.6 15.7 - - + +
432A SER* 3.3 46.0 - - - +
433A THR* 4.5 7.9 - - + -
459A TYR* 5.7 2.5 - - + -
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Residues in contact with THR 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A GLU 2.9 17.7 + - - -
412A PHE 3.1 1.1 + - - -
414A MET* 1.3 87.3 - - - +
416A ALA* 1.3 57.7 + - - +
418A ALA* 3.3 7.6 + - - +
419A ASN* 3.0 27.4 + - - +
431A THR* 4.6 2.9 + - - -
441A ALA* 3.4 11.6 - - - +
444A ALA* 3.7 33.2 - - + +
445A VAL* 3.9 14.8 - - + +
455A GLN* 4.0 15.7 - - - +
457A MET* 4.3 7.4 - - + -
459A TYR* 4.6 6.2 + - - +
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Residues in contact with ALA 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A GLN* 4.3 9.0 - - + +
121A ALA* 3.4 25.4 - - + -
122A ASN* 2.9 30.0 + - - +
162A ILE* 3.7 10.5 - - + -
412A PHE 3.0 15.9 + - - +
413A GLY 4.1 0.2 - - - +
415A THR* 1.3 75.0 - - - +
417A ILE* 1.3 63.9 + - - +
419A ASN* 3.3 10.5 + - - +
420A GLY 3.1 8.0 + - - -
444A ALA* 3.7 10.8 - - + +
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Residues in contact with ILE 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ALA 3.6 19.0 + - - +
124A VAL* 3.9 16.4 - - + -
125A GLY* 3.4 16.0 - - - -
128A ILE* 3.9 13.2 - - + -
166A VAL* 3.7 24.0 - - + -
169A LEU* 3.9 28.0 - - + -
407A TYR* 3.9 17.3 - - + -
410A ARG* 6.4 0.4 - - - -
413A GLY 2.7 31.6 + - - +
414A MET 3.6 3.1 - - - +
416A ALA* 1.3 72.8 - - - +
418A ALA* 1.3 57.7 + - - +
420A GLY* 2.9 18.7 + - - -
421A ILE* 2.9 19.1 + - + +
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Residues in contact with ALA 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407A TYR* 4.3 2.7 - - - +
414A MET 2.9 14.5 + - - +
415A THR 3.4 5.4 - - - +
417A ILE* 1.3 76.3 - - - +
419A ASN* 1.3 58.0 + - - +
421A ILE* 3.1 14.7 + - - +
422A SER* 2.9 27.2 + - - -
429A PRO* 3.7 13.5 - - + +
431A THR* 3.5 22.2 - - + -
455A GLN* 3.4 22.7 - - - +
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Residues in contact with ASN 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A GLN* 4.6 1.6 + - - -
122A ASN* 3.8 9.6 - - - +
415A THR 3.0 16.3 + - - +
416A ALA* 3.4 14.4 - - - +
417A ILE 3.2 0.4 - - - -
418A ALA* 1.3 74.4 - - - +
420A GLY* 1.3 57.7 + - - +
422A SER* 2.9 9.8 + - - -
423A LEU* 2.9 35.4 + - - +
444A ALA* 3.1 26.3 + - - +
447A MET* 4.0 10.1 - - - +
448A ALA* 3.3 23.5 - - - +
451A MET* 3.9 16.7 - - + +
453A GLN* 5.0 1.6 - - + +
455A GLN* 3.1 21.1 + - - -
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Residues in contact with GLY 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ASN* 3.3 31.7 - - - +
125A GLY 4.0 6.5 - - - -
126A MET* 3.5 8.9 - - - +
416A ALA 3.1 7.7 + - - -
417A ILE 2.9 9.4 + - - -
419A ASN* 1.3 76.0 - - - +
421A ILE* 1.3 56.2 + - - +
423A LEU* 3.3 4.9 + - - +
424A HIS* 2.9 29.8 + - - +
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Residues in contact with ILE 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A GLY* 3.5 20.6 - - - +
128A ILE* 4.4 3.8 - - + -
129A ALA* 4.5 5.3 - - + +
376A LEU* 3.9 29.4 - - + +
405A ILE* 3.9 9.2 - - + -
407A TYR* 3.8 22.9 - - - +
417A ILE* 2.9 23.0 + - + +
418A ALA* 3.1 10.7 + - - +
420A GLY* 1.3 75.7 - - - +
422A SER* 1.3 62.4 + - - +
424A HIS* 3.3 15.4 + - - +
425A GLY* 3.6 6.9 + - - +
427A PHE* 3.6 33.5 - - + +
429A PRO* 4.0 16.8 - - + -
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Residues in contact with SER 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418A ALA 2.9 14.4 + - - -
419A ASN* 2.9 18.0 + - - -
421A ILE* 1.3 76.9 - - - +
423A LEU* 1.3 59.9 + - - +
424A HIS 3.4 0.5 + - - -
425A GLY* 3.5 10.6 + - - -
427A PHE 4.8 5.8 - - - +
429A PRO* 3.9 11.2 - - - -
453A GLN* 2.8 35.8 + - - +
454A ARG* 3.5 26.9 - - - -
455A GLN* 5.3 1.5 + - - -
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Residues in contact with LEU 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ARG* 4.8 8.7 + - - -
103A VAL* 4.0 22.7 - - + -
110A GLU* 3.5 21.2 - - - +
111A THR* 3.3 33.4 - - - +
122A ASN* 4.7 2.0 - - - +
126A MET* 4.0 12.1 - - + -
419A ASN 2.9 23.5 + - - +
420A GLY* 3.6 6.3 - - - +
422A SER* 1.3 76.0 + - - +
424A HIS* 1.3 66.0 + - - +
425A GLY* 3.4 0.5 + - - -
451A MET* 3.9 13.9 - - + -
453A GLN* 3.5 28.9 - - + +
675A EDO 5.8 0.3 + - - -
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Residues in contact with HIS 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ALA 4.9 0.2 - - - -
57A ARG* 4.9 1.6 + - - -
59A ARG* 2.9 58.1 + - - +
126A MET* 3.6 28.0 - - + +
129A ALA* 3.5 15.9 - - + +
130A GLU* 4.0 12.3 + - - -
133A LEU* 4.1 17.9 - - + -
147A HIS* 2.8 35.4 + + - -
149A THR* 6.0 0.4 - - - -
329A MET* 3.7 6.1 - - + +
420A GLY 2.9 16.6 + - - +
421A ILE 3.6 6.5 - - - +
422A SER 3.3 0.6 - - - -
423A LEU* 1.3 78.8 - - - +
425A GLY* 1.3 78.5 + - - +
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Residues in contact with GLY 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A LEU* 4.4 0.3 - - - +
329A MET* 3.7 23.4 - - - +
421A ILE 3.6 3.1 + - - -
422A SER 3.5 10.6 + - - -
423A LEU 3.3 3.8 - - - -
424A HIS* 1.3 100.0 + - - +
426A GLY* 1.3 58.7 + - - -
427A PHE* 3.4 12.9 + - - -
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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
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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