Contacts of the helix formed by residues 3105 - 3122 (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 ILE3105 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3102D ILE* 3.6 18.8 - - - -
3103D VAL 2.6 5.2 + - - +
3104D ASN 3.6 0.2 - - - -
3105D ASN* 1.3 84.6 - - - +
3106D PRO* 1.3 66.3 - - - +
3107D PHE* 3.4 34.8 - - - -
3108D LEU* 2.7 45.3 + - + +
3109D ARG* 2.7 23.1 + - - -
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Residues in contact with PRO3106 (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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3105D ILE* 1.3 97.9 - - - +
3107D PHE* 1.3 74.0 + - + +
3109D ARG* 3.1 5.9 + - + +
3110D SER* 2.9 30.9 + - - +
3360D LYS* 5.9 1.6 - - - +
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Residues in contact with PHE3107 (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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3105D ILE* 3.4 32.1 - - - -
3106D PRO* 1.3 82.2 - - + +
3108D LEU* 1.3 68.7 + - + +
3110D SER* 3.8 4.2 - - - -
3111D LEU* 2.6 40.3 + - + +
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Residues in contact with LEU3108 (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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3102D ILE* 5.3 5.2 - - + -
3103D VAL* 3.4 31.4 - - + +
3105D ILE* 2.7 44.3 + - + +
3107D PHE* 1.3 84.6 - - + +
3109D ARG* 1.3 65.0 + - - +
3111D LEU* 3.0 28.3 + - + +
3112D ILE* 2.8 29.3 + - + +
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Residues in contact with ARG3109 (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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3103D VAL* 4.0 15.3 + - + +
3104D ASN* 4.4 21.4 + - - +
3105D ILE 2.7 15.4 + - - +
3106D PRO* 3.5 9.4 - - + +
3108D LEU* 1.3 71.9 - - - +
3110D SER* 1.3 55.4 + - - +
3112D ILE* 2.8 6.6 + - - +
3113D MET 2.8 31.4 + - - -
3346D GLU* 3.8 9.7 + - - -
3357D PHE* 3.3 21.7 - - + -
3358D LYS* 2.7 40.5 + - - +
3359D LEU 3.0 28.9 + - - -
3360D LYS* 3.5 36.4 - - + +
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Residues in contact with SER3110 (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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3106D PRO* 2.9 18.6 + - - +
3107D PHE* 3.8 4.9 - - - -
3109D ARG* 1.3 75.4 - - - +
3111D LEU* 1.3 66.7 + - - +
3112D ILE 2.8 0.5 + - - -
3113D MET* 3.0 8.2 + - - -
3114D LYS* 2.6 30.5 + - - +
3360D LYS* 3.0 24.9 + - - +
3365D LEU* 3.9 23.3 - - - +
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Residues in contact with LEU3111 (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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3107D PHE* 2.6 21.5 + - + +
3108D LEU* 3.1 41.5 - - + +
3110D SER* 1.3 71.7 - - - +
3112D ILE* 1.3 67.9 + - + +
3114D LYS* 3.6 13.3 - - - +
3115D TYR* 3.1 24.5 + - + +
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Residues in contact with ILE3112 (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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3093D LEU* 5.7 3.1 - - + -
3100D TRP* 4.4 18.8 - - + -
3103D VAL* 4.5 14.8 - - + -
3108D LEU* 2.8 24.8 + - + +
3109D ARG* 2.8 6.0 + - - +
3110D SER 2.8 0.6 + - - -
3111D LEU* 1.3 88.4 - - + +
3113D MET* 1.3 59.5 + - - +
3114D LYS 2.9 1.1 - - - -
3115D TYR* 2.4 38.4 + - + +
3116D VAL* 2.7 20.1 + - + +
3357D PHE* 3.3 28.7 - - + -
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Residues in contact with MET3113 (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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3109D ARG 2.8 13.5 + - - +
3110D SER* 3.6 8.7 - - - +
3112D ILE* 1.3 72.2 - - - +
3114D LYS* 1.3 51.9 + - - +
3116D VAL* 3.0 47.5 - - + +
3117D LEU* 2.7 64.2 + - + +
3345D ILE* 5.2 6.1 - - + -
3357D PHE* 3.3 14.0 - - + -
3359D LEU* 3.6 22.7 - - + -
3360D LYS* 3.1 50.0 - - + +
3365D LEU* 3.7 7.9 - - + -
3531D LEU* 4.8 5.4 - - + -
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Residues in contact with LYS3114 (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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3110D SER 2.6 23.4 + - - +
3111D LEU* 3.6 11.8 - - - +
3112D ILE 2.8 0.2 + - - -
3113D MET* 1.3 71.0 - - - +
3115D TYR* 1.3 62.1 + - - +
3117D LEU* 2.6 29.8 + - - +
3118D THR* 2.7 24.6 + - + +
3365D LEU* 4.0 32.1 - - + +
3366D LEU* 6.4 0.2 - - + -
3368D ASN* 4.5 9.3 - - - +
3369D GLN* 3.6 29.2 - - - +
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Residues in contact with TYR3115 (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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3084D PRO* 5.7 4.2 - - - +
3089D VAL* 4.4 22.1 - - + +
3093D LEU* 6.1 2.5 - - + -
3111D LEU* 3.1 10.4 + - + +
3112D ILE* 2.4 30.4 + - + +
3114D LYS* 1.3 79.0 - - - +
3116D VAL* 1.3 67.9 + - + -
3118D THR* 2.8 9.4 + - - -
3119D SER* 2.3 64.2 + - - -
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Residues in contact with VAL3116 (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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3112D ILE* 2.7 28.3 + - + +
3113D MET* 3.0 42.4 - - + +
3115D TYR* 1.3 78.2 - - + +
3117D LEU* 1.3 70.1 + - - +
3119D SER* 2.4 23.3 + - - -
3120D ARG* 3.4 18.8 + - + +
3357D PHE* 4.5 6.5 - - + -
3359D LEU* 4.7 7.4 - - + -
3531D LEU* 4.5 9.9 - - + -
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Residues in contact with LEU3117 (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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3113D MET* 2.7 48.1 + - + +
3114D LYS* 2.6 15.2 + - - +
3116D VAL* 1.3 74.6 - - - +
3118D THR* 1.3 53.6 + - + +
3120D ARG* 3.3 3.6 + - - +
3121D SER* 2.5 29.0 + - - -
3360D LYS 4.7 2.7 - - - +
3365D LEU* 3.8 17.5 - - + -
3366D LEU* 4.3 22.9 - - + -
3531D LEU* 3.6 37.1 - - + +
3535D MET* 4.2 27.4 - - + -
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Residues in contact with THR3118 (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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3114D LYS* 2.7 27.6 + - + +
3115D TYR* 2.8 24.3 + - - -
3117D LEU* 1.3 68.2 - - - +
3119D SER* 1.3 65.4 + - - +
3120D ARG 3.6 0.7 - - - +
3121D SER* 2.6 25.5 + - - +
3122D TYR* 4.2 4.5 + - - +
3366D LEU* 4.8 6.5 - - + -
3369D GLN* 4.0 37.5 - - + +
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Residues in contact with SER3119 (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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3115D TYR* 2.3 56.8 + - - -
3116D VAL* 2.4 23.7 + - - -
3118D THR* 1.3 72.5 + - - +
3120D ARG* 1.3 70.6 + - - +
3122D TYR* 3.2 20.8 - - - -
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Residues in contact with ARG3120 (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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3116D VAL* 3.4 19.2 - - + +
3117D LEU 3.3 5.1 + - - +
3118D THR 3.1 0.6 - - - -
3119D SER* 1.3 85.5 - - - +
3121D SER* 1.3 54.7 - - - +
3122D TYR* 2.5 29.5 + - - -
3123D LEU* 3.1 16.5 + - - +
3355D TYR* 5.0 15.0 + - - -
3523D VAL* 5.4 0.2 - - - +
3524D GLU* 2.8 34.9 + - - -
3527D ALA* 3.0 41.0 - - - +
3528D PRO* 3.6 27.3 - - + +
3531D LEU* 4.7 16.7 - - + +
3701D PGX 4.7 6.1 + - - -
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Residues in contact with SER3121 (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 2.5 21.8 + - - -
3118D THR* 2.6 22.6 + - - -
3120D ARG* 1.3 72.6 - - - +
3122D TYR* 1.3 54.8 + - - -
3123D LEU 2.4 15.3 + - - -
3124D ILE* 3.4 19.6 + - - +
3366D LEU* 6.0 1.0 - - - +
3370D GLN 6.0 1.6 - - - -
3371D PHE* 5.3 15.7 - - - -
3528D PRO* 5.6 0.8 - - - +
3532D LYS* 5.6 6.2 - - - +
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Residues in contact with TYR3122 (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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3044D ARG* 5.1 3.5 + - - -
3083D LYS* 5.6 4.7 - - - +
3118D THR 4.2 3.6 + - - +
3119D SER 3.2 18.6 - - - -
3120D ARG 2.5 23.7 + - - -
3121D SER* 1.3 72.6 - - - +
3123D LEU* 1.3 82.4 + - + +
3124D ILE 4.8 3.0 - - - +
3471D SER* 3.9 13.2 + - - -
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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