Contacts of the helix formed by residues 495 - 507 (chain A) in PDB entry 1IVS
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 TRP 495 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A PHE 4.5 1.3 - - - -
40A MET 4.5 1.8 - - - -
41A PRO* 3.3 34.5 - - + -
42A PRO* 3.8 19.9 - - + +
456A TRP* 4.1 3.8 - + + -
459A SER* 2.9 33.5 + - - -
460A ALA 4.5 0.2 - - - -
462A TRP* 4.1 11.9 - + - +
485A LEU* 4.1 31.9 - - + -
486A VAL 4.8 0.4 - - - -
487A THR* 4.3 9.6 - - - -
491A ILE* 3.1 39.9 + - + +
493A PHE 3.1 1.4 - - - -
494A LEU* 1.3 79.9 - - - +
496A VAL* 1.3 63.6 + - + +
497A SER 3.1 1.0 + - - -
498A ARG* 3.1 3.4 + - - +
499A MET* 2.7 59.5 + - - +
990A VAA 3.1 27.3 - - + +
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Residues in contact with VAL 496 (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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381A PHE* 5.2 0.2 - - + -
390A ASN* 4.6 1.6 - - - +
485A LEU* 3.9 14.6 - - + -
487A THR* 3.8 28.9 - - + -
491A ILE 3.2 3.8 + - - +
492A LEU* 3.6 39.0 - - + +
495A TRP* 1.3 81.7 - - + +
497A SER* 1.3 58.1 + - - +
499A MET* 3.5 6.6 + - - +
500A GLU* 2.8 45.8 + - + +
512A PHE* 4.0 5.4 - - + -
515A VAL* 4.2 25.1 - - + -
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Residues in contact with SER 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A VAL* 5.4 0.2 - - - +
390A ASN* 2.8 25.6 + - - -
393A TRP* 3.9 24.9 - - - -
394A LEU* 4.1 6.5 - - - +
492A LEU 2.9 12.5 + - - -
493A PHE* 3.5 15.8 - - - -
495A TRP 3.2 0.4 - - - -
496A VAL* 1.3 73.9 - - - +
498A ARG* 1.3 60.6 + - - +
500A GLU* 2.7 35.5 + - - +
501A VAL* 3.1 14.8 + - - +
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Residues in contact with ARG 498 (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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184A SER* 4.3 11.3 + - - -
186A LEU* 4.5 11.4 - - - +
363A MET* 5.9 1.3 - - - -
393A TRP* 4.4 20.0 - - - -
400A TRP* 3.2 66.2 - - + +
454A ASP* 4.1 4.0 + - - -
456A TRP* 3.0 33.0 - - - +
460A ALA* 3.3 24.1 - - + +
493A PHE 3.3 20.1 + - - -
494A LEU* 3.4 23.9 + - - +
495A TRP* 3.1 7.8 + - - +
497A SER* 1.3 78.0 - - - +
499A MET* 1.3 61.1 + - - +
501A VAL* 3.3 21.6 - - - +
502A SER* 3.4 5.2 + - - -
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Residues in contact with MET 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A PHE* 5.7 1.8 - - + -
459A SER 3.4 13.9 - - - +
460A ALA* 3.3 21.5 - - - +
462A TRP* 4.3 0.9 - - - -
463A PRO* 3.8 22.7 - - + +
485A LEU* 3.7 20.9 - - + -
495A TRP* 2.7 57.4 + - + +
496A VAL* 3.8 3.1 - - - +
498A ARG* 1.3 69.1 - - - +
500A GLU* 1.3 65.9 + - - +
501A VAL 3.0 1.8 - - - -
502A SER* 3.4 2.6 + - - -
503A GLY 3.0 19.1 + - - -
511A PRO* 3.4 8.6 - - - +
512A PHE* 2.8 43.3 - - + -
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Residues in contact with GLU 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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370A VAL* 3.5 20.2 - - + +
374A LEU* 3.7 20.5 - - - +
379A ILE* 4.0 8.4 - - + +
381A PHE* 4.0 3.8 - - - -
390A ASN* 2.8 33.2 + - - +
394A LEU* 4.4 4.6 - - + +
496A VAL* 2.8 27.0 + - - +
497A SER* 2.7 33.0 + - - +
499A MET* 1.3 72.1 - - - +
501A VAL* 1.3 60.4 + - - +
503A GLY 4.0 0.3 - - - -
504A TYR* 3.1 32.7 + - + +
511A PRO* 3.7 10.3 - - + -
512A PHE* 4.0 17.0 - - + -
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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
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160A TYR* 3.6 20.6 - - - +
361A LEU* 5.7 1.6 - - + -
363A MET* 4.2 17.7 - - + -
366A LEU* 4.1 35.0 - - + -
367A ALA* 4.4 2.0 - - - +
370A VAL* 3.6 20.9 - - + -
394A LEU* 5.3 4.9 - - + -
400A TRP* 6.1 4.0 - - + -
497A SER 3.1 9.9 + - - +
498A ARG* 3.3 14.1 - - - +
500A GLU* 1.3 74.6 - - - +
502A SER* 1.3 72.0 + - - +
503A GLY 2.8 1.6 + - - -
504A TYR* 2.9 3.1 + - - +
505A HIS* 2.8 25.1 + - + +
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Residues in contact with SER 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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160A TYR* 4.4 7.0 + - - -
460A ALA* 2.9 33.3 + - - +
461A LEU* 3.3 26.4 - - - +
463A PRO* 5.9 0.7 - - - -
464A LEU* 4.1 11.1 - - - +
498A ARG 3.4 5.3 + - - -
499A MET 3.4 2.4 + - - -
501A VAL* 1.3 81.5 - - - +
503A GLY* 1.3 57.5 + - - +
505A HIS* 4.8 0.2 - - - -
506A PHE* 2.8 44.6 + - - +
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Residues in contact with GLY 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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463A PRO* 5.7 0.6 - - - +
464A LEU* 4.8 4.4 - - - +
480A TYR* 3.3 16.6 - - - -
499A MET 3.0 9.1 + - - -
501A VAL 2.8 2.0 + - - -
502A SER* 1.3 79.3 - - - +
504A TYR* 1.3 55.8 + - - +
507A MET* 3.3 11.6 + - - +
508A GLY 3.2 15.4 + - - -
509A GLU 2.8 18.1 - - - +
511A PRO* 3.6 15.0 - - - -
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Residues in contact with TYR 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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369A GLU* 3.0 33.5 - - + +
370A VAL* 3.7 31.2 - - + -
372A LYS* 6.0 0.2 - - + -
373A GLY* 3.3 19.0 - - - -
374A LEU* 4.0 2.4 + - + -
376A ARG* 4.4 6.1 - - - -
378A ASP* 2.7 46.9 + - - +
379A ILE* 4.4 10.4 - - + +
500A GLU* 3.1 26.6 + - + +
501A VAL 2.9 6.5 + - - +
503A GLY* 1.3 73.5 - - - -
505A HIS* 1.3 58.5 + - - +
508A GLY* 3.1 22.7 - - - -
509A GLU* 3.9 12.3 - - - +
510A ARG* 3.9 29.0 - - + +
511A PRO* 4.5 4.0 - - + -
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Residues in contact with HIS 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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159A ARG* 4.3 6.9 + - - -
160A TYR* 3.0 42.3 - + - +
163A GLU* 3.3 32.1 + - - -
165A LEU* 3.6 19.7 - - + +
366A LEU* 3.5 12.5 - - + +
369A GLU* 3.0 34.8 + - + +
501A VAL* 2.8 17.0 + - - +
502A SER 4.2 0.9 - - - +
504A TYR* 1.3 80.6 - - - +
506A PHE* 1.3 73.8 + + - +
507A MET 3.4 0.7 - - - -
508A GLY* 4.4 1.3 + - - -
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Residues in contact with PHE 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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156A ALA* 3.2 47.8 - - + -
159A ARG* 3.7 48.9 + - + +
160A TYR* 3.8 24.9 - + - -
163A GLU* 4.5 0.2 - - - -
461A LEU* 4.2 13.7 - - + -
464A LEU* 4.3 4.5 - - + -
469A TRP* 3.5 33.7 + + + +
502A SER* 2.8 26.1 + - - +
505A HIS* 1.3 89.4 - + - +
507A MET* 1.3 68.9 + - - +
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Residues in contact with MET 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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464A LEU* 3.6 26.7 - - + -
469A TRP* 3.7 23.1 - - - -
476A LEU* 4.0 26.5 - - + -
480A TYR* 3.8 30.7 - - + +
502A SER 4.8 0.2 - - - +
503A GLY 3.3 12.4 + - - +
506A PHE* 1.3 87.8 - - + +
508A GLY* 1.3 67.3 + - - +
509A GLU* 3.3 5.6 + - - +
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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