Contacts of the helix formed by residues 3312 - 3328 (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 ASN3312 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3308A TRP* 2.8 54.9 + - + +
3309A LEU* 3.3 9.0 - - - +
3311A ASP* 1.3 86.2 - - - +
3313A PRO* 1.3 64.6 - - - +
3314A GLU* 3.2 5.5 + - + -
3315A THR* 3.2 21.0 + - - +
3316A ALA* 3.0 17.5 + - - +
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Residues in contact with PRO3313 (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* 4.9 9.6 - - - +
3309A LEU 3.9 7.2 - - - +
3310A LYS 3.6 14.1 - - - +
3311A ASP 3.2 11.4 - - - +
3312A ASN* 1.3 84.2 - - - +
3314A GLU* 1.3 78.8 + - + +
3316A ALA* 3.5 5.8 - - + +
3317A LYS* 3.0 38.5 + - + +
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Residues in contact with GLU3314 (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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3312A ASN* 4.7 3.1 - - + -
3313A PRO* 1.3 100.2 - - + +
3315A THR* 1.3 63.5 + - - +
3317A LYS* 3.5 9.7 + - - +
3318A GLU* 3.3 20.1 + - - +
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Residues in contact with THR3315 (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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3293A TYR* 3.5 37.2 - - + +
3308A TRP* 4.0 18.0 - - + -
3312A ASN* 3.2 26.5 + - - +
3314A GLU* 1.3 76.6 - - - +
3316A ALA* 1.3 65.6 + - - +
3318A GLU* 3.2 12.9 + - - +
3319A ILE* 3.0 30.7 + - + +
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Residues in contact with ALA3316 (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* 3.7 30.3 - - + +
3274A LEU* 3.7 14.0 - - + +
3309A LEU* 3.8 19.4 - - + +
3312A ASN 3.0 13.4 + - - +
3313A PRO* 3.5 10.1 - - + +
3314A GLU 3.3 0.2 - - - -
3315A THR* 1.3 76.5 - - - +
3317A LYS* 1.3 59.9 + - - +
3319A ILE* 3.3 2.1 + - - -
3320A GLU* 2.9 31.6 + - - +
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Residues in contact with LYS3317 (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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3270A PHE* 4.8 9.9 - - - -
3271A TYR* 5.2 8.2 + - - -
3313A PRO* 3.0 27.1 + - + +
3314A GLU* 3.7 8.1 - - - +
3316A ALA* 1.3 78.4 - - - +
3318A GLU* 1.3 57.5 + - - +
3320A GLU* 2.9 28.0 + - - +
3321A LYS* 2.9 33.8 + - - +
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Residues in contact with GLU3318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3293A TYR* 2.7 26.3 + - - +
3294A LYS* 3.7 17.7 + - - -
3314A GLU 3.3 10.2 + - - +
3315A THR* 3.2 15.5 + - - +
3316A ALA 3.2 0.4 - - - -
3317A LYS* 1.3 77.9 - - - +
3319A ILE* 1.3 64.7 - - - +
3321A LYS* 3.4 7.6 + - - +
3322A LYS* 3.2 45.5 + - - +
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Residues in contact with ILE3319 (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* 4.3 12.3 - - + -
3278A GLY* 4.6 2.7 - - - -
3283A LEU* 4.1 22.7 - - + -
3284A ILE* 4.3 19.7 - - + -
3293A TYR* 3.8 46.4 - - + +
3298A ILE* 6.2 0.2 - - + -
3308A TRP* 5.3 0.9 - - + -
3309A LEU* 3.9 24.0 - - + -
3315A THR* 3.0 18.6 + - + +
3316A ALA 3.9 3.4 - - - +
3318A GLU* 1.3 71.3 - - - +
3320A GLU* 1.3 66.3 + - - +
3322A LYS* 3.2 8.8 + - - +
3323A VAL* 2.9 29.3 + - + +
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Residues in contact with GLU3320 (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* 3.9 18.4 - - + -
3270A PHE* 3.7 22.6 - - + -
3274A LEU* 3.7 16.9 - - + +
3316A ALA 2.9 16.6 + - - +
3317A LYS* 2.9 36.2 + - - +
3319A ILE* 1.3 76.7 - - - +
3321A LYS* 1.3 62.6 + - - +
3323A VAL* 3.1 3.7 + - - +
3324A ARG* 2.9 55.7 + - - +
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Residues in contact with LYS3321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3317A LYS* 2.9 19.6 + - - +
3318A GLU* 3.7 7.9 - - - +
3319A ILE 3.3 0.2 - - - -
3320A GLU* 1.3 75.3 - - - +
3322A LYS* 1.3 58.7 + - + +
3324A ARG* 3.5 9.8 + - - +
3325A GLU* 3.0 47.2 + - + +
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Residues in contact with LYS3322 (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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3283A LEU* 3.7 27.6 - - + -
3293A TYR* 4.5 5.2 + - - +
3294A LYS* 5.7 2.2 - - - +
3318A GLU* 3.2 41.0 + - + +
3319A ILE* 3.2 10.2 + - - +
3321A LYS* 1.3 78.3 - - + +
3323A VAL* 1.3 59.3 + - - +
3325A GLU* 3.3 16.2 + - - +
3326A LEU* 2.9 35.7 + - + +
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Residues in contact with VAL3323 (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* 4.2 9.0 - - + -
3049A ILE* 4.1 20.4 - - + -
3274A LEU* 4.6 4.3 - - + -
3277A LEU* 4.0 23.8 - - + +
3278A GLY* 4.4 16.2 - - - +
3281A GLU* 5.0 2.7 - - + -
3283A LEU* 3.8 17.3 - - + -
3319A ILE* 2.9 27.3 + - + +
3320A GLU* 3.6 9.2 - - - +
3322A LYS* 1.3 74.1 - - - +
3324A ARG* 1.3 58.4 + - - +
3326A LEU* 3.2 7.5 + - - +
3327A LEU* 2.9 38.5 + - + +
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Residues in contact with ARG3324 (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* 4.4 9.1 + - - -
3045A LEU* 3.9 19.1 - - + +
3048A ASP* 2.8 33.8 + - - +
3049A ILE* 5.5 3.4 - - + -
3054A GLY* 3.4 31.1 + - - -
3270A PHE* 5.5 1.8 - - - -
3320A GLU* 2.9 47.7 + - - +
3321A LYS* 3.7 7.6 - - - +
3323A VAL* 1.3 74.1 - - + +
3325A GLU* 1.3 61.6 + - + +
3327A LEU* 5.2 0.7 - - - +
3328A LEU* 2.8 60.3 + - + +
3331A PRO* 5.9 0.2 - - - +
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Residues in contact with GLU3325 (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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3321A LYS* 3.0 45.1 + - + +
3322A LYS* 3.6 16.0 - - - +
3324A ARG* 1.3 75.6 - - - +
3326A LEU* 1.3 64.2 + - + +
3327A LEU 3.6 0.2 + - - -
3328A LEU 4.5 6.6 + - - +
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Residues in contact with LEU3326 (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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3281A GLU* 3.8 43.5 - - + +
3283A LEU* 4.4 18.8 - - + -
3322A LYS* 2.9 22.9 + - + +
3323A VAL* 3.6 4.3 - - - +
3325A GLU* 1.3 80.6 - - + +
3327A LEU* 1.3 66.4 + - + +
3328A LEU 5.3 0.4 - - - +
2282D LYS* 4.9 7.0 - - - +
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Residues in contact with LEU3327 (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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3049A ILE* 3.8 34.8 - - + +
3256A LYS* 5.2 3.3 + - - -
3277A LEU* 3.8 28.0 - - + -
3280A LYS* 5.2 8.7 - - - +
3281A GLU* 3.6 40.6 - - + +
3323A VAL* 2.9 21.5 + - + +
3326A LEU* 1.3 85.6 - - - +
3328A LEU* 1.3 64.8 + - - +
3329A SER* 3.4 4.5 + - - -
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Residues in contact with LEU3328 (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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3048A ASP 3.4 26.5 - - - +
3049A ILE* 3.8 18.8 - - + -
3052A GLY 3.8 7.9 - - - +
3053A ALA 4.5 4.3 - - - +
3054A GLY* 3.6 17.7 - - - +
3324A ARG* 2.8 61.0 + - + +
3325A GLU 4.5 5.7 - - - +
3326A LEU 5.3 0.5 - - - -
3327A LEU* 1.3 71.0 - - - +
3329A SER* 1.3 62.0 + - - +
3330A ASN 3.5 2.1 + - - +
3331A PRO* 3.9 28.4 - - + +
3332A ASN 5.8 0.2 - - - +
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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
------------------------------------------------------------
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