Contacts of the helix formed by residues 496 - 515 (chain A) in PDB entry 5I74
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 496 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A ILE* 5.6 0.4 - - - -
171A TYR* 5.9 1.6 - - + -
491A LEU 3.5 1.3 + - - +
492A LEU* 3.2 22.0 + - + +
494A GLU 3.5 1.4 - - - -
495A TYR* 1.3 80.1 - - - +
497A THR* 1.3 71.3 + - + +
498A GLY 3.4 0.9 - - - -
499A PRO* 3.5 4.3 - - - +
500A ALA* 3.5 22.5 + - - +
578A GLY* 3.6 19.7 - - - +
581A ILE* 4.1 22.0 - - + -
582A GLY* 4.0 9.4 - - - +
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Residues in contact with THR 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ILE* 4.5 10.0 - - + +
171A TYR* 3.9 27.1 - - + -
172A ILE* 4.0 13.7 - - + -
175A TYR* 3.1 37.5 + - + -
492A LEU* 2.7 27.5 + - + +
493A GLU* 3.2 6.2 + - - -
496A ALA* 1.3 74.6 - - + +
498A GLY* 1.3 58.8 + - - +
500A ALA* 3.3 2.3 + - - +
501A VAL* 2.9 33.1 + - - +
700A 69D 3.3 9.6 + - - -
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Residues in contact with GLY 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A PHE* 3.5 16.4 - - - -
493A GLU 3.2 3.8 + - - -
497A THR* 1.3 81.4 + - - +
499A PRO* 1.3 63.5 - - - +
501A VAL 3.2 2.1 + - - -
502A LEU* 2.9 26.4 + - - +
700A 69D 3.7 13.9 - - - -
703A D12 3.7 20.9 - - - -
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Residues in contact with PRO 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A GLU 3.4 18.8 - - - +
495A TYR 3.8 12.1 - - - +
496A ALA 3.5 15.5 - - - +
498A GLY* 1.3 90.0 - - - +
500A ALA* 1.3 49.8 + - - +
502A LEU* 4.4 4.7 - - + -
503A THR* 2.4 38.4 + - - +
553A ILE* 3.3 13.4 - - + +
556A PHE* 3.5 35.9 - - + -
557A LEU* 5.3 4.3 - - + -
579A TYR* 5.1 4.0 - - + -
582A GLY* 6.0 1.1 - - - -
703A D12 3.9 4.5 - - + -
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Residues in contact with ALA 500 (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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168A ILE* 3.5 29.6 - - + +
496A ALA 3.5 13.4 + - - +
497A THR 3.3 1.0 + - - -
498A GLY 3.2 0.8 - - - -
499A PRO* 1.3 76.3 - - - +
501A VAL* 1.3 61.6 + - - +
503A THR* 3.6 7.1 - - - -
504A VAL* 2.9 31.2 + - - +
582A GLY* 4.1 8.7 - - - +
585A SER* 3.7 12.6 - - - +
586A PHE* 4.2 11.9 - - + -
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Residues in contact with VAL 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ILE* 3.6 27.4 - - + -
172A ILE* 4.2 1.6 - - + -
334A PHE* 4.3 18.2 - - + -
335A PHE* 4.5 7.0 - - + -
339A PRO 5.1 6.5 - - - +
340A GLY 5.9 0.4 - - - +
341A PHE* 4.4 14.4 - - + -
497A THR 2.9 23.9 + - - +
498A GLY 3.7 3.1 - - - +
500A ALA* 1.3 74.3 - - - +
502A LEU* 1.3 60.0 + - - +
504A VAL* 3.2 8.8 - - + +
505A ALA* 2.9 29.9 + - + +
700A 69D 4.0 28.9 - - + -
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Residues in contact with LEU 502 (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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334A PHE* 3.5 37.2 - - + -
335A PHE* 3.5 23.6 - - + -
498A GLY 2.9 13.3 + - - +
499A PRO* 4.5 0.7 - - + -
501A VAL* 1.3 76.9 - - - +
503A THR* 1.3 57.7 + - - +
505A ALA* 3.7 1.9 - - - +
506A LEU* 2.9 27.9 + - - +
549A LEU* 4.2 15.0 - - + +
552A ILE* 3.6 43.5 - - + -
553A ILE* 3.5 24.4 - - + +
703A D12 3.8 16.8 - - + -
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Residues in contact with THR 503 (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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499A PRO* 2.4 27.3 + - - +
500A ALA* 3.6 8.9 - - - -
501A VAL 3.2 0.2 - - - -
502A LEU* 1.3 76.6 - - - +
504A VAL* 1.3 59.7 + - - +
506A LEU* 2.9 10.2 + - + +
507A ILE* 2.9 41.9 + - + +
553A ILE* 3.3 16.6 - - + +
586A PHE* 5.0 22.1 - - + -
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Residues in contact with VAL 504 (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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161A ILE* 3.6 39.5 - - + +
164A ALA* 4.8 9.6 - - + -
165A ILE* 4.1 18.4 - - + -
168A ILE* 5.5 6.3 - - + -
340A GLY 4.4 9.4 - - - +
341A PHE* 5.8 2.0 - - + -
500A ALA 2.9 21.6 + - - +
501A VAL* 3.2 16.6 - - + +
503A THR* 1.3 77.9 - - - +
505A ALA* 1.3 60.7 + - - +
507A ILE* 3.2 8.3 + - + +
508A GLU* 2.9 35.2 + - - +
586A PHE* 6.1 3.8 - - + -
589A ILE* 6.5 0.7 - - + -
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Residues in contact with ALA 505 (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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132A LEU* 5.5 0.6 - - + +
334A PHE* 3.6 30.1 - - + -
339A PRO 4.5 0.4 - - - +
340A GLY* 4.4 19.9 - - - +
501A VAL* 2.9 20.1 + - + +
502A LEU 3.7 3.6 - - - +
504A VAL* 1.3 79.1 - - - +
506A LEU* 1.3 56.1 + - - +
508A GLU* 3.4 5.8 + - - +
509A ALA* 2.9 30.5 + - - +
549A LEU* 3.4 8.7 - - + +
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Residues in contact with LEU 506 (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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502A LEU 2.9 15.1 + - - +
503A THR* 2.9 12.5 + - + +
505A ALA* 1.3 73.9 - - - +
507A ILE* 1.3 69.2 + - + +
509A ALA* 3.4 1.1 + - + +
510A VAL* 2.9 51.3 + - + +
546A PRO* 3.3 35.2 - - + +
549A LEU* 3.7 19.0 - - + +
550A LEU* 4.0 25.8 - - + +
553A ILE* 5.2 6.5 - - + -
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Residues in contact with ILE 507 (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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158A PHE* 4.7 14.8 - - + -
161A ILE* 3.5 23.6 - - + -
503A THR* 2.9 28.4 + - + +
504A VAL* 3.6 9.6 - - + +
506A LEU* 1.3 86.0 - - + +
508A GLU* 1.3 58.3 + - - +
510A VAL* 3.9 5.3 - - + +
511A ALA* 2.9 30.5 + - - +
589A ILE* 3.9 22.9 - - + -
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Residues in contact with GLU 508 (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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135A MET* 5.3 2.7 - - + -
136A GLU* 3.6 11.6 - - - +
151A TRP* 3.5 31.2 + - + -
161A ILE* 3.3 23.8 - - + +
165A ILE* 3.3 10.7 - - - +
340A GLY* 2.9 40.7 - - - +
342A GLY* 4.9 1.9 + - - -
504A VAL* 2.9 19.0 + - - +
505A ALA* 3.8 4.7 - - - +
506A LEU 3.2 0.2 - - - -
507A ILE* 1.3 74.6 - - - +
509A ALA* 1.3 61.0 + - - +
511A ALA 3.1 0.2 + - - -
512A VAL* 2.9 40.2 + - + +
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Residues in contact with ALA 509 (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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132A LEU* 4.1 24.2 - - + -
135A MET* 4.4 13.1 - - + +
505A ALA 2.9 17.4 + - - +
506A LEU* 3.9 3.8 - - - +
508A GLU* 1.3 76.5 - - - +
510A VAL* 1.3 62.1 + - - +
512A VAL* 4.7 0.3 - - - +
513A SER* 3.4 24.8 + - - -
541A TRP 5.0 0.3 - - - +
545A SER* 5.3 0.2 - - - -
546A PRO* 4.2 23.7 - - + +
549A LEU* 4.2 8.5 - - + -
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Residues in contact with VAL 510 (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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158A PHE* 6.4 0.9 - - + -
506A LEU* 2.9 42.9 + - + +
507A ILE* 4.0 4.9 - - - +
509A ALA* 1.3 77.9 - - - +
511A ALA* 1.3 60.0 + - - +
513A SER* 5.1 0.2 - - - -
514A TRP* 2.9 63.2 + - + +
515A PHE* 3.9 9.4 + - + -
546A PRO* 4.4 12.8 - - + -
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Residues in contact with ALA 511 (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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151A TRP* 3.6 22.2 - - + -
154A ILE* 5.7 0.2 - - - -
155A CYS* 4.6 1.7 - - - -
158A PHE* 3.5 34.5 - - + -
507A ILE 2.9 19.9 + - - +
508A GLU 3.1 0.4 + - - +
510A VAL* 1.3 78.7 - - - +
512A VAL* 1.3 63.0 + - - +
515A PHE* 3.1 32.9 + - + +
516A TYR* 3.3 4.9 + - - +
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Residues in contact with VAL 512 (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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135A MET* 3.8 30.1 - - + -
139A LEU* 3.7 34.1 - - + -
151A TRP* 4.5 15.0 - - + -
154A ILE* 5.5 4.7 - - + -
508A GLU* 2.9 19.8 + - + +
509A ALA 4.7 1.1 - - - +
511A ALA* 1.3 76.1 - - - +
513A SER* 1.3 63.2 + - - +
516A TYR* 3.8 14.8 - - + +
517A GLY 3.3 24.1 + - - +
518A ILE* 4.9 2.0 - - + -
521A PHE* 4.6 10.8 - - + -
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Residues in contact with SER 513 (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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509A ALA 3.4 18.7 + - - -
511A ALA 3.3 0.2 - - - -
512A VAL* 1.3 80.4 - - - +
514A TRP* 1.3 79.4 + - - +
517A GLY* 3.3 21.1 - - - -
518A ILE* 3.3 23.2 + - - +
541A TRP* 3.2 27.2 + - - -
542A VAL* 3.6 9.0 - - - +
546A PRO* 5.1 0.9 - - - -
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Residues in contact with TRP 514 (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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510A VAL* 2.9 41.6 + - + +
513A SER* 1.3 91.7 + - - +
515A PHE* 1.3 69.1 + - + +
517A GLY* 4.5 0.9 - - - -
542A VAL* 3.2 32.6 + - + +
543A ALA* 5.6 1.6 - - - -
546A PRO* 4.7 18.4 - - + -
547A LEU* 6.2 5.8 - - + -
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Residues in contact with PHE 515 (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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155A CYS* 3.6 25.1 - - + -
157A ILE* 4.9 10.5 - - + -
158A PHE* 4.2 28.7 - + - -
510A VAL* 4.5 9.9 - - + -
511A ALA* 3.1 19.8 + - - +
513A SER 3.5 0.4 - - - -
514A TRP* 1.3 87.5 - - + +
516A TYR* 1.3 66.8 + - - +
517A GLY* 3.0 2.2 + - - -
612A ILE* 4.8 25.5 - - + +
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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
------------------------------------------------------------
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