Contacts of the helix formed by residues 3312 - 3328 (chain D) in PDB entry 3CMT
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 ASN3312 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3308D TRP* 2.8 54.0 + - + +
3309D LEU* 3.3 9.2 - - - +
3310D LYS 3.4 0.2 - - - -
3311D ASP* 1.3 88.0 - - - +
3313D PRO* 1.3 61.6 - - - +
3314D GLU* 3.2 6.9 + - + -
3315D THR* 3.2 21.1 + - - +
3316D ALA* 3.0 22.2 + - - +
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Residues in contact with PRO3313 (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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3271D TYR* 4.8 10.3 - - - +
3309D LEU 3.7 6.9 - - - +
3310D LYS 3.6 14.1 - - - +
3311D ASP 3.2 11.9 - - - +
3312D ASN* 1.3 84.7 - - - +
3314D GLU* 1.3 78.9 + - + +
3316D ALA* 3.5 5.8 - - + +
3317D LYS* 3.0 38.6 + - + +
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Residues in contact with GLU3314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3312D ASN* 4.7 2.9 - - + -
3313D PRO* 1.3 99.9 - - + +
3315D THR* 1.3 64.0 + - - +
3317D LYS* 3.5 9.2 + - - +
3318D GLU* 3.3 19.9 + - - +
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Residues in contact with THR3315 (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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3293D TYR* 3.4 37.5 - - + +
3308D TRP* 4.0 18.6 - - + -
3312D ASN* 3.2 26.1 + - - +
3314D GLU* 1.3 76.1 - - - +
3316D ALA* 1.3 61.1 + - - +
3318D GLU* 3.2 12.6 + - - +
3319D ILE* 3.0 35.9 + - + +
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Residues in contact with ALA3316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3271D TYR* 3.7 30.1 - - + +
3274D LEU* 3.6 13.2 - - + +
3309D LEU* 3.8 19.6 - - + +
3312D ASN 3.0 13.4 + - - +
3313D PRO* 3.5 10.1 - - + +
3314D GLU 3.3 0.2 - - - -
3315D THR* 1.3 76.7 - - - +
3317D LYS* 1.3 60.6 + - - +
3319D ILE* 3.3 2.1 + - - +
3320D GLU* 2.8 32.1 + - - +
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Residues in contact with LYS3317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3270D PHE* 4.8 9.4 - - - -
3271D TYR* 5.2 7.9 + - - -
3313D PRO* 3.0 26.1 + - + +
3314D GLU* 3.6 8.3 - - - +
3316D ALA* 1.3 79.5 - - - +
3318D GLU* 1.3 57.2 + - - +
3320D GLU* 2.9 26.9 + - - +
3321D LYS* 2.9 33.4 + - - +
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Residues in contact with GLU3318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3293D TYR* 2.7 26.5 + - - +
3294D LYS* 3.7 17.3 + - - -
3314D GLU 3.3 10.2 + - - +
3315D THR* 3.2 16.1 + - - +
3316D ALA 3.2 0.4 - - - -
3317D LYS* 1.3 76.7 - - - +
3319D ILE* 1.3 64.0 + - - +
3321D LYS* 3.4 8.0 + - - +
3322D LYS* 3.3 45.8 + - - +
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Residues in contact with ILE3319 (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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3274D LEU* 4.3 13.5 - - + -
3278D GLY* 4.6 2.5 - - - -
3283D LEU* 4.1 22.9 - - + -
3284D ILE* 4.3 19.5 - - + -
3293D TYR* 3.8 45.8 - - + +
3298D ILE* 6.2 0.4 - - + -
3308D TRP* 5.3 0.7 - - + -
3309D LEU* 3.9 23.8 - - + -
3315D THR* 3.0 18.3 + - + +
3316D ALA 3.8 3.4 - - - +
3318D GLU* 1.3 71.9 - - - +
3320D GLU* 1.3 67.0 + - - +
3322D LYS* 3.2 9.0 + - - +
3323D VAL* 2.9 30.1 + - + +
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Residues in contact with GLU3320 (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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3045D LEU* 4.3 7.4 - - + +
3270D PHE* 3.7 26.4 - - + -
3274D LEU* 3.7 19.9 - - + +
3316D ALA 2.8 16.8 + - - +
3317D LYS* 2.9 36.5 + - - +
3319D ILE* 1.3 77.7 - - - +
3321D LYS* 1.3 57.1 + - - +
3323D VAL* 3.1 4.7 + - - +
3324D ARG* 2.8 65.5 + - - +
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Residues in contact with LYS3321 (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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3317D LYS* 2.9 19.7 + - - +
3318D GLU* 3.7 8.1 - - - +
3319D ILE 3.3 0.2 - - - -
3320D GLU* 1.3 76.7 - - - +
3322D LYS* 1.3 58.9 + - + +
3324D ARG* 3.5 9.4 + - - +
3325D GLU* 3.0 49.0 + - + +
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Residues in contact with LYS3322 (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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3283D LEU* 3.7 24.9 - - + -
3293D TYR* 4.5 5.2 + - - +
3294D LYS* 5.8 1.8 - - - +
3318D GLU* 3.3 41.9 + - + +
3319D ILE* 3.2 9.5 + - - +
3321D LYS* 1.3 77.3 - - + +
3323D VAL* 1.3 60.6 + - - +
3325D GLU* 3.3 15.9 + - - +
3326D LEU* 2.9 38.0 + - + +
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Residues in contact with VAL3323 (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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3045D LEU* 3.9 23.3 - - + -
3049D ILE* 4.3 4.5 - - + -
3274D LEU* 4.6 4.9 - - + -
3277D LEU* 4.0 19.1 - - + +
3278D GLY* 4.4 14.6 - - - +
3281D GLU* 5.0 2.9 - - + -
3283D LEU* 3.8 17.3 - - + -
3319D ILE* 2.9 27.5 + - + +
3320D GLU* 3.1 8.9 + - - +
3322D LYS* 1.3 74.5 - - - +
3324D ARG* 1.3 58.4 + - - +
3326D LEU* 3.3 7.9 + - - +
3327D LEU* 2.9 44.3 + - + +
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Residues in contact with ARG3324 (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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3041D SER* 4.7 8.3 + - - -
3045D LEU* 3.4 30.7 - - + +
3048D ASP* 3.7 19.0 + - - +
3049D ILE* 5.7 1.3 - - - -
3054D GLY* 4.7 10.5 + - - -
3270D PHE* 5.5 3.0 - - - -
3320D GLU* 2.8 48.1 + - - +
3321D LYS* 3.7 7.6 - - - +
3323D VAL* 1.3 74.3 - - - +
3325D GLU* 1.3 61.1 + - - +
3327D LEU* 4.5 0.4 - - - +
3328D LEU* 2.8 74.0 + - + +
3331D PRO* 4.5 0.8 - - - +
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Residues in contact with GLU3325 (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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3321D LYS* 3.0 45.2 + - + +
3322D LYS* 3.6 16.0 - - - +
3324D ARG* 1.3 76.1 - - + +
3326D LEU* 1.3 63.7 + - + +
3327D LEU 3.6 0.2 + - - -
3328D LEU 4.5 6.4 + - - +
3331D PRO* 5.3 8.4 - - + +
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Residues in contact with LEU3326 (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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2282A LYS* 5.1 5.8 - - - +
3281D GLU* 3.9 42.8 - - + +
3283D LEU* 4.4 17.7 - - + -
3322D LYS* 2.9 24.9 + - + +
3323D VAL* 3.6 4.5 - - - +
3325D GLU* 1.3 78.4 - - + +
3327D LEU* 1.3 66.1 + - + +
3328D LEU 5.3 0.8 - - - +
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Residues in contact with LEU3327 (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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3049D ILE* 3.5 36.7 - - + +
3256D LYS* 5.8 1.6 + - - -
3277D LEU* 3.8 28.7 - - + -
3280D LYS* 5.2 8.5 - - - +
3281D GLU* 3.6 40.8 - - + +
3323D VAL* 2.9 21.2 + - + +
3326D LEU* 1.3 86.1 - - - +
3328D LEU* 1.3 63.7 + - - +
3329D SER* 3.3 4.0 + - - -
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Residues in contact with LEU3328 (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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3048D ASP* 4.0 22.2 - - + +
3049D ILE* 4.0 20.0 - - + +
3052D GLY 5.0 1.8 - - - +
3054D GLY* 4.0 19.1 - - - +
3324D ARG* 2.8 64.3 + - + +
3325D GLU 4.6 5.2 - - - +
3326D LEU 5.3 0.5 - - - -
3327D LEU* 1.3 69.6 - - - +
3329D SER* 1.3 67.3 + - - +
3330D ASN 3.3 1.2 + - - -
3331D PRO* 3.5 42.4 - - + +
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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