Contacts of the helix formed by residues 3269 - 3281 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3260A PHE* 5.3 1.2 - - - +
3261A GLN* 2.9 41.5 + - + +
3263A LEU* 4.0 25.6 - - + +
3266A GLU* 5.3 6.0 - - - +
3267A GLY 3.4 1.8 + - - -
3268A ILE* 1.3 71.2 - - - +
3270A PHE* 1.3 59.7 + - - +
3271A TYR* 3.7 2.3 + - - +
3272A GLY* 2.9 33.0 + - - -
3273A GLU* 3.3 21.1 + - - +
3302A LYS* 5.0 5.1 - - - +
3306A THR* 3.8 14.9 + - - +
3310A LYS* 5.7 2.6 + - - -
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Residues in contact with PHE3270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3041A SER* 5.3 6.1 - - - -
3043A GLY* 3.5 26.2 - - - +
3044A SER 4.6 0.9 - - - -
3045A LEU* 3.7 26.4 - - + +
3048A ASP* 5.6 0.2 - - - -
3268A ILE* 2.9 10.2 + - - +
3269A ASN* 1.3 70.9 + - - +
3271A TYR* 1.3 93.6 + + + +
3273A GLU* 3.2 19.9 + - - +
3274A LEU* 3.0 32.0 + - + +
3316A ALA* 6.3 0.2 - - + -
3317A LYS* 4.8 7.0 - - - -
3320A GLU* 3.7 38.4 - - + -
3324A ARG* 5.5 1.8 - - - -
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Residues in contact with TYR3271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3269A ASN* 3.5 1.8 + - - +
3270A PHE* 1.3 95.8 - + + +
3272A GLY* 1.3 60.2 + - - +
3274A LEU* 3.5 14.1 - - + +
3275A VAL* 2.9 33.4 + - - +
3306A THR* 3.6 24.5 - - + +
3309A LEU* 3.8 29.0 + - + +
3310A LYS* 3.5 39.0 + - + -
3313A PRO* 4.9 10.7 - - - +
3316A ALA* 3.7 23.6 - - + +
3317A LYS* 5.2 8.7 + - - -
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Residues in contact with GLY3272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3269A ASN* 2.9 30.2 + - - -
3270A PHE 3.2 0.2 - - - -
3271A TYR* 1.3 76.1 - - - +
3273A GLU* 1.3 62.4 + - - +
3275A VAL* 3.3 2.9 + - - +
3276A ASP* 3.2 14.4 + - - -
3302A LYS* 2.9 32.3 + - - -
3306A THR* 3.6 10.6 - - - +
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Residues in contact with GLU3273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3044A SER* 2.5 32.6 + - - -
3045A LEU* 2.9 27.3 + - + +
3046A SER* 2.8 22.0 + - - +
3259A GLU 4.9 2.5 - - - +
3260A PHE* 3.6 21.0 - - + +
3268A ILE* 3.9 2.4 - - - +
3269A ASN 3.3 10.7 + - - +
3270A PHE* 3.2 22.5 + - - +
3272A GLY* 1.3 74.9 - - - +
3274A LEU* 1.3 54.6 + - - +
3276A ASP* 3.1 6.5 + - - -
3277A LEU* 2.8 50.0 + - + +
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Residues in contact with LEU3274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3045A LEU* 3.8 20.8 - - + +
3270A PHE* 3.0 17.2 + - + +
3271A TYR* 3.2 19.7 + - + +
3273A GLU* 1.3 78.6 - - - +
3275A VAL* 1.3 57.2 + - - +
3277A LEU* 3.8 0.4 - - - -
3278A GLY* 2.8 28.4 + - - -
3284A ILE* 4.3 1.9 - - - +
3309A LEU* 4.0 17.3 - - + -
3316A ALA* 3.7 38.6 - - + +
3319A ILE* 4.3 12.1 - - + +
3320A GLU* 3.7 33.0 - - + +
3323A VAL* 4.6 4.5 - - + -
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Residues in contact with VAL3275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3271A TYR 2.9 18.6 + - - +
3272A GLY 3.5 7.2 - - - +
3274A LEU* 1.3 74.4 - - - +
3276A ASP* 1.3 64.8 + - - +
3278A GLY* 3.1 2.1 + - - -
3279A VAL* 2.8 31.2 + - + +
3284A ILE* 4.1 12.0 - - + +
3291A TYR* 3.7 35.0 - - + -
3298A ILE* 5.7 0.4 - - + -
3302A LYS* 4.2 11.7 - - + -
3305A ALA* 4.0 8.3 - - + -
3306A THR* 3.8 27.8 - - - +
3309A LEU* 3.7 18.2 - - + -
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Residues in contact with ASP3276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3272A GLY 3.2 2.1 + - - +
3273A GLU* 3.1 10.5 + - - +
3275A VAL* 1.3 79.9 - - - +
3277A LEU* 1.3 62.1 + - + +
3279A VAL* 3.5 5.8 + - - +
3280A LYS* 3.0 30.2 + - - +
3291A TYR* 5.2 1.9 + - - -
3302A LYS* 3.2 43.8 + - - +
1235D GLU* 5.4 8.0 - - - +
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Residues in contact with LEU3277 (chain A).
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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3045A LEU* 4.0 10.3 - - + -
3046A SER* 4.2 19.7 - - - -
3049A ILE* 4.0 18.2 - - + -
3273A GLU* 2.8 43.5 + - + +
3274A LEU 4.0 2.7 - - - +
3276A ASP* 1.3 75.4 - - + +
3278A GLY* 1.3 58.9 + - - +
3280A LYS* 3.4 16.8 + - + +
3281A GLU* 3.0 35.0 + - - +
3323A VAL* 4.0 14.8 - - + -
3327A LEU* 3.8 26.9 - - + -
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Residues in contact with GLY3278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3274A LEU 2.8 18.3 + - - -
3275A VAL 3.5 0.9 - - - -
3277A LEU* 1.3 74.1 - - - +
3279A VAL* 1.3 62.1 + - - +
3281A GLU* 3.3 2.0 + - - -
3282A LYS 3.2 3.3 + - - -
3283A LEU* 2.9 36.6 + - - -
3284A ILE* 3.1 19.7 + - - -
3319A ILE* 4.6 2.2 - - - -
3323A VAL* 4.4 10.0 - - - +
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Residues in contact with VAL3279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3275A VAL* 2.8 21.7 + - + +
3276A ASP* 3.9 5.2 - - - +
3278A GLY* 1.3 71.4 - - - +
3280A LYS* 1.3 63.3 + - - +
3282A LYS* 3.1 21.0 + - - +
3284A ILE* 3.5 26.2 - - + +
3286A LYS* 4.2 24.2 - - + -
3291A TYR* 3.6 34.8 - - + -
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Residues in contact with LYS3280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3276A ASP 3.0 19.1 + - - +
3277A LEU* 3.6 19.9 - - + +
3279A VAL* 1.3 79.1 - - - +
3281A GLU* 1.3 76.6 + - - +
3282A LYS* 3.3 14.1 + - - +
3327A LEU* 5.2 8.9 - - - +
2280D LYS* 4.5 25.9 - - + +
2282D LYS* 4.4 5.5 - - - -
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Residues in contact with GLU3281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3277A LEU 3.0 20.3 + - - +
3278A GLY 4.1 2.7 - - - +
3279A VAL 3.2 0.4 - - - -
3280A LYS* 1.3 93.4 + - + +
3282A LYS* 1.3 70.5 + - - +
3283A LEU* 3.2 18.0 + - + +
3323A VAL* 5.0 5.4 - - + -
3326A LEU* 3.8 30.2 - - + +
3327A LEU* 3.6 44.5 - - + +
2282D LYS* 2.7 37.1 + - - +
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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