Contacts of the helix formed by residues 3444 - 3458 (chain D) in PDB entry 1DDX
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 VAL3444 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3388D HIS* 3.5 42.2 - - + +
3391D LEU* 3.2 35.0 - - + -
3404D PHE* 4.0 9.6 - - + -
3440D VAL* 3.6 11.4 - - + -
3441D PRO* 3.5 15.4 - - + +
3442D ILE 3.1 0.4 - - - -
3443D ALA* 1.3 78.8 - - - +
3445D GLN* 1.3 67.8 + - - +
3446D ALA 3.4 1.1 - - - -
3447D VAL* 3.0 24.7 + - + -
3448D ALA* 3.3 2.7 + - - +
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Residues in contact with GLN3445 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3175D LYS* 5.9 2.4 - - - +
3178D LEU* 4.2 21.1 - - + +
3179D GLU* 5.3 5.0 - - - +
3183D LEU* 3.3 32.2 - - + +
3440D VAL* 5.3 0.4 - - - -
3441D PRO 3.4 5.2 + - - -
3442D ILE* 2.8 34.2 + - + +
3443D ALA 3.0 3.0 - - - +
3444D VAL* 1.3 79.1 - - - +
3446D ALA* 1.3 64.3 + - - +
3447D VAL 3.1 0.3 + - - -
3448D ALA* 3.3 4.3 + - - +
3449D LYS* 3.2 19.1 + - - +
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Residues in contact with ALA3446 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3443D ALA 4.3 5.5 + - - +
3444D VAL 3.4 1.1 - - - -
3445D GLN* 1.3 76.5 - - - +
3447D VAL* 1.3 70.4 + - + +
3449D LYS* 3.2 10.9 + - - +
3450D ALA* 3.0 17.8 + - - +
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Residues in contact with VAL3447 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3386D HIS* 5.8 0.2 - - + -
3388D HIS* 2.9 34.5 - - + +
3444D VAL* 3.0 20.1 + - + +
3446D ALA* 1.3 78.8 - - + +
3448D ALA* 1.3 57.9 + - - +
3450D ALA* 2.6 33.4 + - + +
3451D SER* 2.8 13.3 + - - +
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Residues in contact with ALA3448 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3178D LEU* 4.5 10.3 - - + -
3182D LEU* 5.2 2.9 - - + -
3388D HIS* 3.6 20.0 - - + +
3440D VAL* 3.8 24.9 - - + -
3444D VAL 3.3 2.9 + - - +
3445D GLN 3.8 7.2 - - - +
3447D VAL* 1.3 79.3 - - - +
3449D LYS* 1.3 61.1 + - - +
3451D SER* 3.2 23.5 - - - -
3452D ILE* 2.8 19.3 - - + +
3504D TYR* 3.6 7.0 - - + +
3508D LEU* 5.5 0.2 - - + -
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Residues in contact with LYS3449 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3173D ASP* 5.5 1.5 + - - -
3174D SER* 2.9 32.6 + - - +
3175D LYS* 4.0 17.3 - - + +
3178D LEU* 3.9 21.7 - - + +
3445D GLN 3.2 9.9 + - - +
3446D ALA* 3.2 14.1 + - - +
3447D VAL 2.8 4.6 + - - -
3448D ALA* 1.3 70.5 - - - +
3450D ALA* 1.3 67.3 + - - +
3452D ILE* 2.7 23.4 + - - +
3453D ASP* 2.8 32.8 + - - +
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Residues in contact with ALA3450 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3446D ALA 3.0 10.4 + - - +
3447D VAL* 2.6 17.6 + - - +
3449D LYS* 1.3 69.9 - - - +
3451D SER* 1.3 55.9 + - - +
3452D ILE 2.4 14.4 + - - -
3453D ASP* 2.6 26.9 + - - -
3454D GLN* 2.7 31.6 + - + +
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Residues in contact with SER3451 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3383D THR* 4.2 7.1 - - - +
3386D HIS* 3.4 27.3 - - - -
3388D HIS* 3.4 11.8 - - - -
3447D VAL* 2.8 16.4 + - - +
3448D ALA* 3.2 18.2 - - - -
3450D ALA* 1.3 74.0 - - - +
3452D ILE* 1.3 49.3 + - - +
3454D GLN* 3.9 9.0 - - - +
3455D SER* 2.6 28.9 + - - -
3504D TYR* 3.2 25.1 - - - -
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Residues in contact with ILE3452 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3174D SER* 4.3 20.2 - - - +
3177D VAL* 5.7 4.7 - - + -
3178D LEU* 4.6 4.7 - - + +
3182D LEU* 4.0 22.9 - - + -
3448D ALA 2.8 23.8 - - - +
3449D LYS* 2.7 21.9 + - + +
3450D ALA 2.4 4.4 + - - -
3451D SER* 1.3 68.6 - - - +
3453D ASP* 1.3 69.1 + - - +
3454D GLN 3.1 0.7 - - - -
3455D SER* 3.1 14.9 + - - -
3456D ARG* 3.3 29.0 + - - +
3495D TYR* 5.3 0.4 - - - +
3502D GLU* 3.1 27.3 - - - +
3504D TYR* 3.7 17.7 - - + -
3505D PRO* 4.6 9.6 - - + -
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Residues in contact with ASP3453 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3174D SER* 2.8 26.3 + - - -
3449D LYS* 2.8 41.1 + - - +
3450D ALA* 2.6 20.3 + - - +
3452D ILE* 1.3 70.8 - - - +
3454D GLN* 1.3 60.3 + - + +
3456D ARG* 2.8 33.6 - - - +
3457D GLU* 3.0 13.7 + - + +
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Residues in contact with GLN3454 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3212D THR* 6.3 0.8 - - - +
3214D HIS* 4.9 16.8 + - - -
3218D PRO* 3.8 23.0 - - + +
3382D ASN* 5.9 0.6 + - - -
3386D HIS* 4.8 10.9 + - - -
3450D ALA* 2.7 43.2 + - + +
3451D SER* 3.9 9.6 - - - +
3453D ASP* 1.3 66.3 - - + +
3455D SER* 1.3 54.9 + - - +
3456D ARG 2.6 5.4 + - - -
3457D GLU* 2.4 55.1 + - - +
3458D MET* 2.9 13.4 + - - +
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Residues in contact with SER3455 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3383D THR* 4.5 9.2 - - - +
3451D SER 2.6 22.9 + - - -
3452D ILE* 3.1 9.3 + - - +
3454D GLN* 1.3 75.1 - - - +
3456D ARG* 1.3 56.2 + - - +
3458D MET* 3.8 2.0 - - - -
3459D LYS 3.3 2.6 + - - -
3460D TYR* 2.7 74.3 + - - +
3502D GLU* 5.4 3.2 + - - -
3504D TYR* 4.5 7.1 - - - +
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Residues in contact with ARG3456 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3162D PRO* 6.5 0.4 - - + -
3163D MET* 6.1 5.8 - - + -
3171D LEU* 3.1 29.8 + - + +
3172D PRO* 2.8 32.0 + - - +
3173D ASP* 4.8 0.6 - - - +
3174D SER* 4.6 7.2 - - - +
3177D VAL* 4.7 4.0 - - - +
3452D ILE* 3.3 30.6 + - - +
3453D ASP* 2.8 17.2 + - - +
3454D GLN 2.6 4.2 + - - -
3455D SER* 1.3 74.1 - - - +
3457D GLU* 1.3 54.6 + - - +
3459D LYS* 2.7 33.5 + - - +
3460D TYR 4.8 0.7 - - - +
3495D TYR* 3.7 11.5 + - - -
3502D GLU* 2.5 47.9 + - - +
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Residues in contact with GLU3457 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3218D PRO* 3.7 19.7 - - + +
3453D ASP* 3.0 15.0 + - + +
3454D GLN* 2.4 56.0 + - - +
3456D ARG* 1.3 68.3 - - - +
3458D MET* 1.3 53.3 + - + +
3459D LYS* 2.6 31.9 + - - +
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Residues in contact with MET3458 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3132D VAL* 4.2 17.9 - - + -
3148D TYR* 5.2 0.4 - - + -
3150D ARG* 2.7 31.9 + - - +
3154D PRO* 4.1 2.8 - - - +
3218D PRO* 2.9 57.2 - - + +
3219D GLY* 3.0 13.2 - - - +
3379D SER* 3.1 28.3 - - - +
3382D ASN* 6.1 1.1 - - - +
3383D THR* 5.6 0.9 - - - -
3454D GLN* 2.9 13.2 + - + +
3455D SER* 3.9 5.4 - - - +
3457D GLU* 1.3 73.5 - - - +
3459D LYS* 1.3 69.2 + - - +
3460D TYR* 2.7 24.8 + - + -
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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