Contacts of the helix formed by residues 3301 - 3312 (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 GLY3301 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1233A GLU* 4.9 12.1 - - - -
3289D ALA* 2.8 22.7 + - - +
3291D TYR* 3.5 9.5 - - - -
3300D GLN* 1.3 73.7 - - - +
3302D LYS* 1.3 67.8 + - - -
3303D ALA* 3.1 4.9 - - - -
3304D ASN 3.0 13.9 + - - -
3305D ALA 3.2 7.6 + - - -
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Residues in contact with LYS3302 (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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1233A GLU* 5.0 10.2 + - - +
1234A GLY* 6.5 0.4 - - - -
3241D GLU* 6.0 0.4 - - - -
3261D GLN* 4.2 27.7 - - - +
3269D ASN* 5.4 0.4 - - - +
3272D GLY* 2.9 41.4 + - - -
3275D VAL* 4.2 10.5 - - + +
3276D ASP* 3.2 33.0 + - - +
3291D TYR* 3.3 23.4 + - - +
3301D GLY* 1.3 70.5 - - - -
3303D ALA* 1.3 58.3 + - - +
3305D ALA* 3.4 2.7 + - - +
3306D THR* 2.7 38.5 + - - +
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Residues in contact with ALA3303 (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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1303A ALA* 6.4 1.8 - - + -
3300D GLN 5.5 0.4 - - - +
3301D GLY* 3.0 2.8 + - - +
3302D LYS* 1.3 79.0 - - - +
3304D ASN* 1.3 65.3 + - - +
3306D THR* 3.5 6.7 - - - -
3307D ALA* 3.3 20.3 + - - +
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Residues in contact with ASN3304 (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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1304A ASN* 3.3 37.9 + - - +
3298D ILE 4.1 1.0 - - - +
3299D GLY* 4.0 6.3 - - - -
3300D GLN* 2.9 36.6 + - - +
3301D GLY 3.0 2.8 + - - -
3303D ALA* 1.3 80.5 - - - +
3305D ALA* 1.3 61.1 + - - +
3306D THR 3.2 0.4 - - - -
3307D ALA* 3.1 12.1 + - - +
3308D TRP* 2.9 28.1 + - - +
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Residues in contact with ALA3305 (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* 4.0 16.4 - - + -
3291D TYR* 3.8 39.9 - - + -
3298D ILE* 4.1 20.5 - - + +
3299D GLY* 4.3 2.3 - - - -
3301D GLY 3.2 3.2 + - - -
3302D LYS 3.8 7.2 - - - +
3304D ASN* 1.3 77.2 - - - +
3306D THR* 1.3 60.8 + - - +
3308D TRP* 3.3 4.0 + - - +
3309D LEU* 3.2 26.2 + - - +
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Residues in contact with THR3306 (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 14.5 + - - +
3271D TYR* 3.6 11.2 - - + +
3272D GLY* 3.6 35.2 - - - +
3275D VAL* 3.9 11.0 - - - +
3302D LYS* 2.7 26.4 + - - +
3303D ALA* 3.5 8.6 - - - -
3304D ASN 3.2 0.2 - - - -
3305D ALA* 1.3 76.6 - - - +
3307D ALA* 1.3 61.1 + - - +
3309D LEU* 3.2 5.9 + - - +
3310D LYS* 3.2 32.8 + - - +
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Residues in contact with ALA3307 (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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3303D ALA 3.3 9.5 + - - +
3304D ASN* 3.1 17.5 + - - +
3306D THR* 1.3 79.6 - - - +
3308D TRP* 1.3 61.9 + - - +
3310D LYS* 3.4 15.1 - - + +
3311D ASP* 3.1 29.9 + - - +
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Residues in contact with TRP3308 (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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3293D TYR* 4.7 8.3 - + + -
3296D GLU* 3.8 26.8 + - - -
3297D LYS 5.1 0.8 + - - -
3298D ILE* 3.2 67.0 - - + +
3304D ASN 2.9 7.1 + - - +
3305D ALA 3.5 7.9 - - - +
3307D ALA* 1.3 77.6 - - - +
3309D LEU* 1.3 81.7 + - + +
3311D ASP* 3.1 7.2 + - + +
3312D ASN* 2.8 67.3 + - + +
3315D THR* 4.0 27.4 - - + -
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Residues in contact with LEU3309 (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* 3.8 23.6 - - + +
3274D LEU* 4.0 21.3 - - + -
3275D VAL* 3.7 31.9 - - + +
3284D ILE* 4.8 8.1 - - + -
3298D ILE* 5.0 4.5 - - + -
3305D ALA 3.2 5.5 + - - +
3306D THR 3.2 8.5 + - - +
3308D TRP* 1.3 93.2 - - + +
3310D LYS* 1.3 65.1 + - - +
3312D ASN 3.3 19.8 - - - +
3313D PRO* 3.7 1.7 - - - +
3316D ALA* 3.8 27.6 - - - +
3319D ILE* 3.9 24.5 - - + -
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Residues in contact with LYS3310 (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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3263D LEU* 6.3 0.2 - - - -
3266D GLU* 2.7 32.0 + - - -
3269D ASN* 5.7 1.9 + - - -
3271D TYR* 3.5 37.5 + - + -
3306D THR* 3.2 25.2 + - - +
3307D ALA* 3.4 17.0 - - + +
3309D LEU* 1.3 76.9 - - - +
3311D ASP* 1.3 65.0 + - - +
3312D ASN 3.5 0.2 + - - -
3313D PRO* 3.6 15.6 - - - +
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Residues in contact with ASP3311 (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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3307D ALA* 3.1 15.2 + - - +
3308D TRP* 3.1 14.5 + - + +
3310D LYS* 1.3 84.7 - - - +
3312D ASN* 1.3 65.9 + - - +
3313D PRO* 3.2 9.4 - - - +
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Residues in contact with ASN3312 (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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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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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