Contacts of the helix formed by residues 3269 - 3281 (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 ASN3269 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3261D GLN* 2.6 54.1 + - + +
3263D LEU* 3.5 30.0 - - + +
3266D GLU* 5.1 6.1 - - - +
3267D GLY 3.0 5.1 + - - -
3268D ILE* 1.3 68.3 - - - +
3270D PHE* 1.3 61.3 + - - +
3271D TYR* 3.7 1.9 + - - +
3272D GLY* 2.9 27.1 + - - -
3273D GLU* 3.3 21.5 + - - +
3302D LYS* 5.0 0.8 - - - +
3306D THR* 3.7 15.2 + - - +
3310D LYS* 5.7 1.4 + - - -
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Residues in contact with PHE3270 (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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3043D GLY 3.8 20.4 - - - +
3044D SER 5.2 0.2 - - - -
3045D LEU* 4.0 24.6 - - + +
3268D ILE 2.7 11.9 + - - +
3269D ASN* 1.3 70.0 + - - +
3271D TYR* 1.3 92.7 + + + +
3273D GLU* 3.2 20.2 + - - +
3274D LEU* 3.0 32.7 + - + +
3317D LYS* 4.8 7.9 - - - -
3320D GLU* 3.7 38.1 - - + -
3324D ARG* 5.5 2.7 - - - -
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Residues in contact with TYR3271 (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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3269D ASN* 3.7 1.7 + - - +
3270D PHE* 1.3 95.0 - + + +
3272D GLY* 1.3 60.5 + - - +
3274D LEU* 3.2 14.8 + - + +
3275D VAL* 3.0 33.1 + - - +
3306D THR* 3.6 24.5 - - + +
3309D LEU* 3.8 27.8 + - + +
3310D LYS* 3.5 38.0 + - + -
3313D PRO* 4.8 10.4 - - - +
3316D ALA* 3.7 24.1 - - + +
3317D LYS* 5.2 8.4 + - - -
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Residues in contact with GLY3272 (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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3261D GLN* 6.1 0.7 - - - -
3269D ASN* 2.9 28.9 + - - -
3271D TYR* 1.3 77.7 - - - +
3273D GLU* 1.3 60.5 + - - +
3275D VAL* 3.3 2.9 + - - +
3276D ASP* 3.2 14.6 + - - -
3302D LYS* 2.9 32.9 + - - -
3306D THR* 3.6 10.9 - - - +
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Residues in contact with GLU3273 (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 SER* 2.4 31.1 + - - -
3045D LEU* 3.3 24.3 + - + -
3046D SER* 3.1 15.5 + - - +
3259D GLU 4.6 2.2 - - - +
3260D PHE* 3.4 27.7 - - + +
3261D GLN 5.2 0.2 - - - +
3268D ILE* 3.5 17.6 - - - +
3269D ASN 3.3 7.2 + - - +
3270D PHE* 3.2 18.6 + - - +
3272D GLY* 1.3 73.7 - - - +
3274D LEU* 1.3 56.2 + - - +
3276D ASP* 3.1 6.6 + - - -
3277D LEU* 2.8 50.5 + - + +
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Residues in contact with LEU3274 (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* 4.2 17.0 - - + +
3270D PHE* 3.0 17.7 + - + +
3271D TYR* 3.2 19.7 + - + +
3273D GLU* 1.3 76.8 - - - +
3275D VAL* 1.3 58.2 + - - +
3277D LEU* 4.6 2.5 - - - -
3278D GLY* 2.8 28.1 + - - -
3284D ILE* 4.2 1.9 - - - +
3309D LEU* 4.0 17.9 - - + -
3316D ALA* 3.6 38.6 - - + +
3319D ILE* 4.3 12.1 - - + -
3320D GLU* 3.7 33.9 - - + +
3323D VAL* 4.6 5.2 - - + -
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Residues in contact with VAL3275 (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 3.0 19.1 + - - +
3272D GLY 3.6 7.4 - - - +
3274D LEU* 1.3 74.4 - - - +
3276D ASP* 1.3 65.1 + - - +
3278D GLY* 3.1 1.7 + - - -
3279D VAL* 2.8 31.4 + - + +
3284D ILE* 4.1 11.5 - - + +
3291D TYR* 3.7 33.9 - - + -
3302D LYS* 4.2 11.0 - - + -
3305D ALA* 4.0 9.0 - - + -
3306D THR* 3.9 27.4 - - - +
3309D LEU* 3.7 18.2 - - + -
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Residues in contact with ASP3276 (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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3272D GLY 3.2 2.4 + - - +
3273D GLU* 3.1 10.4 + - - +
3275D VAL* 1.3 78.5 - - - +
3277D LEU* 1.3 61.0 + - + +
3279D VAL* 3.5 5.6 + - - +
3280D LYS* 3.0 30.8 + - - +
3291D TYR* 5.1 1.9 + - - -
3302D LYS* 3.2 42.5 + - - +
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Residues in contact with LEU3277 (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* 4.4 7.6 - - + -
3046D SER* 4.0 27.4 - - - +
3049D ILE* 4.3 9.0 - - + -
3259D GLU 5.8 1.3 - - - +
3273D GLU* 2.8 41.2 + - + +
3274D LEU* 4.0 4.3 - - - +
3276D ASP* 1.3 73.9 - - + +
3278D GLY* 1.3 59.6 + - - +
3280D LYS* 3.6 16.6 - - + +
3281D GLU* 3.0 34.8 + - - +
3323D VAL* 4.0 22.0 - - + -
3327D LEU* 3.8 27.8 - - + -
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Residues in contact with GLY3278 (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 2.8 19.0 + - - -
3275D VAL 3.6 0.7 - - - -
3277D LEU* 1.3 74.2 - - - +
3279D VAL* 1.3 61.4 + - - +
3281D GLU* 3.3 2.1 + - - -
3282D LYS 3.2 3.5 + - - -
3283D LEU* 2.9 36.9 + - - +
3284D ILE* 3.7 19.3 - - - -
3319D ILE* 4.6 2.5 - - - -
3323D VAL* 4.4 9.4 - - - +
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Residues in contact with VAL3279 (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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3275D VAL 2.8 19.5 + - - +
3276D ASP* 3.9 6.7 - - - +
3278D GLY* 1.3 75.0 - - - +
3280D LYS* 1.3 63.4 + - - +
3282D LYS* 3.1 21.1 + - - +
3284D ILE* 3.5 25.5 - - + +
3286D LYS* 4.2 24.2 - - + -
3291D TYR* 3.6 35.2 - - + -
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Residues in contact with LYS3280 (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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2280A LYS* 4.7 11.1 - - + +
2282A LYS* 4.4 5.9 - - - -
3276D ASP 3.0 19.8 + - - +
3277D LEU* 3.6 20.3 - - + +
3278D GLY 3.3 0.2 - - - -
3279D VAL* 1.3 78.8 - - - +
3281D GLU* 1.3 75.2 + - - +
3282D LYS* 3.2 13.6 + - - +
3327D LEU* 5.2 9.1 - - - +
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Residues in contact with GLU3281 (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* 2.7 37.1 + - - +
3277D LEU 3.0 20.6 + - - +
3278D GLY 3.3 2.7 + - - +
3279D VAL 3.2 0.2 - - - -
3280D LYS* 1.3 96.4 - - + +
3282D LYS* 1.3 70.1 + - - +
3283D LEU* 3.2 17.4 + - + +
3323D VAL* 5.0 5.2 - - + -
3326D LEU* 3.9 31.5 - - + +
3327D LEU* 3.6 43.1 - - + +
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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