Contacts of the helix formed by residues 3519 - 3536 (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 GLY3519 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3435D ALA* 3.3 7.9 - - - +
3507D LEU 5.3 0.2 + - - -
3510D GLU* 2.9 23.5 + - - -
3511D LYS 4.1 4.9 - - - -
3512D PRO* 4.1 14.4 - - - -
3513D ARG* 3.5 14.0 + - - -
3518D PHE* 1.3 86.8 - - - +
3520D GLU* 1.3 65.1 + - - +
3522D MET* 4.5 2.4 - - - +
3523D VAL* 3.7 4.7 + - - +
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Residues in contact with GLU3520 (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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3086D PRO* 4.1 9.3 - - + +
3087D ASN* 3.7 20.5 + - - +
3467D ARG* 2.4 49.8 + - - -
3472D LEU* 4.0 21.5 - - + +
3473D LYS 5.5 0.5 + - - -
3475D TYR* 3.2 10.6 + - - +
3510D GLU* 2.9 4.9 + - - +
3511D LYS 5.1 1.2 + - - -
3513D ARG* 2.9 37.5 - - - +
3519D GLY* 1.3 71.4 - - - -
3521D THR* 1.3 68.0 + - - +
3523D VAL* 2.9 4.7 + - - +
3524D GLU* 2.8 24.4 + - + +
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Residues in contact with THR3521 (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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3463D LEU* 4.3 7.4 - - + +
3467D ARG* 2.5 39.9 + - + +
3472D LEU* 4.2 7.6 - - + +
3475D TYR* 4.4 2.6 - - - -
3503D LEU* 4.0 15.3 - - + -
3507D LEU* 3.1 27.1 - - + -
3510D GLU* 2.7 24.0 + - + -
3520D GLU* 1.3 75.2 + - - +
3522D MET* 1.3 67.7 + - - +
3523D VAL 3.0 0.2 + - - -
3524D GLU* 3.1 9.4 + - - +
3525D LEU* 3.2 20.9 + - + +
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Residues in contact with MET3522 (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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3384D LEU* 3.3 35.2 - - + +
3387D TRP* 2.9 33.4 - - + -
3434D VAL* 5.6 2.2 - - - -
3504D TYR* 6.3 0.4 - - + -
3507D LEU* 3.0 46.2 - - + +
3508D LEU* 6.4 1.6 - - + -
3510D GLU* 3.6 7.5 + - - +
3518D PHE* 3.7 33.7 - - + -
3519D GLY 4.8 0.4 - - - +
3520D GLU 3.4 0.8 - - - -
3521D THR* 1.3 78.7 - - - +
3523D VAL* 1.3 65.8 + - - +
3525D LEU* 4.0 3.5 - - - +
3526D GLY 3.3 15.9 + - - -
3701D PGX 3.7 16.1 - - + +
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Residues in contact with VAL3523 (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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3090D HIS* 5.8 1.3 - - + +
3120D ARG* 5.1 0.9 - - - +
3352D LEU 5.5 1.8 - - - +
3353D SER* 6.3 0.4 - - - -
3355D TYR* 4.8 9.9 - - - +
3513D ARG* 3.5 27.6 - - - +
3518D PHE* 4.1 14.6 - - + +
3519D GLY 3.7 7.3 + - - +
3520D GLU 2.9 9.0 + - - +
3522D MET* 1.3 81.5 - - - +
3524D GLU* 1.3 74.1 + - - +
3525D LEU 2.9 1.0 + - - -
3527D ALA* 2.9 34.2 + - + +
3701D PGX 3.7 41.1 - - + +
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Residues in contact with GLU3524 (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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3086D PRO* 4.0 23.8 - - + +
3120D ARG* 2.8 35.8 + - - -
3123D LEU* 4.5 2.3 - - - +
3470D PHE* 3.1 23.3 - - + +
3472D LEU* 3.8 35.4 - - + -
3513D ARG* 5.0 1.3 - - - +
3520D GLU* 2.8 20.6 + - + +
3521D THR 3.9 2.5 - - - +
3523D VAL* 1.3 88.9 - - + +
3525D LEU* 1.3 58.7 + - - +
3527D ALA* 4.5 0.4 - - - -
3528D PRO* 3.4 11.1 - - - +
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Residues in contact with LEU3525 (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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3380D GLU* 5.3 1.6 - - + -
3384D LEU* 3.5 35.7 - - + -
3466D TYR* 3.9 18.2 - - + +
3470D PHE* 3.2 48.5 - - + -
3472D LEU* 4.7 6.3 - - + -
3503D LEU* 4.4 20.6 - - + -
3521D THR* 3.2 21.1 + - + +
3522D MET 4.0 1.3 - - - +
3523D VAL 2.9 1.0 + - - -
3524D GLU* 1.3 79.3 - - - +
3526D GLY* 1.3 64.5 + - - +
3527D ALA 3.2 1.3 - - - -
3528D PRO* 2.8 18.0 - - - +
3529D PHE* 3.3 25.2 + - + +
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Residues in contact with GLY3526 (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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3381D PHE* 3.8 18.8 - - - -
3384D LEU* 3.9 1.4 - - - +
3522D MET 3.3 7.1 + - - -
3525D LEU* 1.3 78.4 - - - +
3527D ALA* 1.3 60.2 + - - +
3530D SER* 2.8 36.0 + - - -
3701D PGX 3.3 28.3 - - - -
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Residues in contact with ALA3527 (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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3120D ARG* 3.0 42.1 - - - +
3523D VAL 2.9 18.2 + - - +
3524D GLU* 4.1 2.2 - - - +
3526D GLY* 1.3 80.2 - - - +
3528D PRO* 1.3 72.7 - - + +
3530D SER* 3.8 1.8 - - - -
3531D LEU* 3.1 24.5 + - - +
3701D PGX 3.9 13.6 - - - +
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Residues in contact with PRO3528 (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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3120D ARG* 4.0 19.5 - - + +
3121D SER 5.6 0.7 - - - +
3123D LEU* 3.3 37.2 - - + -
3124D ILE* 3.3 24.1 - - + +
3470D PHE* 3.8 4.5 - - + -
3524D GLU 3.4 9.6 - - - +
3525D LEU 2.8 26.0 - - - +
3527D ALA* 1.3 87.7 - - + +
3529D PHE* 1.3 69.2 + - - +
3530D SER 2.6 2.8 + - - -
3531D LEU* 3.0 9.8 + - + +
3532D LYS* 3.2 10.0 + - - +
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Residues in contact with PHE3529 (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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3124D ILE* 3.0 33.2 - - + +
3151D ALA* 3.3 34.1 - - + -
3375D ASN* 4.4 2.3 - - - +
3378D ALA* 3.8 20.9 - - + -
3380D GLU* 3.5 9.4 - - + -
3381D PHE* 3.0 62.0 - + + -
3384D LEU* 4.1 5.8 - - + -
3469D ARG* 6.2 0.4 - - - -
3470D PHE* 3.8 17.9 - + - -
3525D LEU* 3.3 22.1 + - + +
3528D PRO* 1.3 77.3 - - - +
3530D SER* 1.3 61.5 + - - +
3532D LYS* 3.4 12.8 - - - +
3533D GLY* 3.8 4.0 + - - -
3701D PGX 4.9 1.2 - - - +
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Residues in contact with SER3530 (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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3349D VAL* 4.8 2.6 - - - +
3381D PHE* 3.9 3.1 - - - -
3526D GLY 2.8 24.5 + - - -
3527D ALA* 3.8 3.1 - - - -
3528D PRO 2.6 4.2 + - - -
3529D PHE* 1.3 68.1 - - - +
3531D LEU* 1.3 59.7 + - - +
3532D LYS 2.5 17.9 + - - -
3533D GLY 3.2 3.5 + - - -
3534D LEU* 2.9 32.4 + - - +
3701D PGX 3.0 47.9 + - - +
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Residues in contact with LEU3531 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3113D MET* 4.8 4.7 - - + -
3116D VAL* 4.5 14.6 - - + -
3117D LEU* 3.6 34.2 - - + +
3120D ARG* 4.7 20.6 - - + +
3345D ILE* 4.4 17.3 - - + -
3349D VAL* 5.3 12.1 - - + -
3359D LEU* 6.2 3.6 - - + -
3371D PHE* 4.7 2.3 - - - -
3527D ALA* 3.1 14.6 + - - +
3528D PRO* 3.0 7.5 + - + +
3530D SER* 1.3 85.5 + - - +
3532D LYS* 1.3 62.4 + - - +
3534D LEU* 3.8 16.4 - - + -
3535D MET* 3.1 26.5 - - + +
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Residues in contact with LYS3532 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3121D SER* 5.6 6.7 - - - +
3124D ILE* 3.8 31.9 - - + -
3126D SER* 3.2 31.7 + - - -
3371D PHE* 3.4 26.7 - - + -
3372D GLN* 2.8 32.7 + - - +
3374D GLN 3.4 12.5 + - - +
3375D ASN* 3.2 10.8 - - - +
3528D PRO 3.2 7.3 + - - +
3529D PHE* 3.4 12.1 - - - +
3530D SER 2.5 4.6 + - - -
3531D LEU* 1.3 71.0 - - - +
3533D GLY* 1.3 53.6 + - - +
3534D LEU 2.3 17.2 + - - -
3535D MET 2.6 16.3 + - - -
3536D GLY* 2.6 14.7 + - - +
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Residues in contact with GLY3533 (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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3227D GLY* 4.9 3.7 - - - -
3228D VAL* 3.2 22.2 + - - +
3375D ASN* 2.7 38.3 + - - -
3529D PHE 3.8 2.0 + - - -
3530D SER 3.2 3.0 + - - -
3532D LYS* 1.3 70.5 - - - +
3534D LEU* 1.3 59.4 + - - +
3536D GLY* 4.4 2.7 - - - -
3537D ASN* 4.1 9.5 + - - +
3701D PGX 3.5 18.8 - - - -
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Residues in contact with LEU3534 (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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3205D PHE* 4.9 2.2 - - + -
3228D VAL* 4.2 7.9 - - + -
3341D ILE* 3.1 65.9 - - + +
3344D VAL* 3.8 22.9 - - + -
3345D ILE* 3.5 26.9 - - + -
3349D VAL* 4.8 1.6 - - + -
3530D SER* 2.9 34.8 + - - +
3531D LEU* 3.8 11.2 - - + -
3532D LYS 2.3 13.9 + - - -
3533D GLY* 1.3 70.8 - - - +
3535D MET* 1.3 64.3 + - - +
3537D ASN* 3.7 1.9 - - - +
3540D CYS* 3.7 4.5 - - - -
3701D PGX 3.5 17.9 - - + +
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Residues in contact with MET3535 (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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3117D LEU* 4.2 28.7 - - + -
3345D ILE* 4.1 9.2 - - + -
3360D LYS 5.6 0.2 - - - +
3361D PHE* 3.5 42.2 - - + -
3362D ASP 4.1 7.2 - - - +
3363D PRO* 4.0 24.5 - - + -
3366D LEU* 3.8 21.8 - - + -
3371D PHE* 3.5 15.0 - - + -
3373D TYR* 3.7 3.5 - - - -
3531D LEU* 3.1 18.6 + - + +
3532D LYS 2.6 6.5 + - - -
3534D LEU* 1.3 76.7 - - + +
3536D GLY* 1.3 53.3 + - - +
3537D ASN 2.5 19.4 + - - +
3540D CYS* 3.0 25.0 - - + +
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Residues in contact with GLY3536 (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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3371D PHE* 3.0 26.0 - - - -
3373D TYR* 3.2 6.3 - - - +
3374D GLN* 3.1 40.0 + - - -
3375D ASN* 4.4 2.9 + - - +
3532D LYS 2.6 19.3 + - - -
3533D GLY 4.9 2.0 - - - -
3535D MET* 1.3 66.9 - - - +
3537D ASN* 1.3 61.0 + - - -
3538D PRO* 3.6 3.3 - - - +
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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