Contacts of the helix formed by residues 3071 - 3085 (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 GLY3071 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3069A SER 3.4 2.6 - - - -
3070A SER* 1.3 80.2 - - - +
3072A LYS* 1.3 61.6 + - - +
3073A THR 3.5 2.2 - - - -
3074A THR* 3.8 0.4 - - - -
3075A LEU* 2.9 34.0 + - - +
3225A ILE* 3.8 7.5 - - - +
3262A ILE* 4.0 13.7 - - - +
3502A ADP 3.0 24.9 + - - -
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Residues in contact with LYS3072 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3064A ILE* 4.3 11.9 - - + +
3065A TYR* 3.9 2.7 - - - -
3066A GLY 3.5 20.2 + - - +
3067A PRO 2.8 30.1 + - - -
3070A SER* 3.5 8.5 - - - +
3071A GLY* 1.3 71.8 - - - +
3073A THR* 1.3 61.8 + - - +
3075A LEU* 3.8 2.6 - - - +
3076A THR* 3.0 24.8 + - - -
3192A ILE* 3.6 27.6 - - + +
3193A ASN 3.4 25.8 - - - +
3194A GLN* 5.0 0.9 - - - +
3225A ILE* 3.6 16.8 - - + -
3501A ALF 3.4 22.1 - - - -
3502A ADP 2.7 35.0 + - - +
4217A PHE* 3.9 4.0 - - - -
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Residues in contact with THR3073 (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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3072A LYS* 1.3 73.6 - - - +
3074A THR* 1.3 67.5 + - - +
3076A THR* 3.1 4.3 + - - -
3077A LEU* 2.8 42.9 + - + +
3092A PHE* 4.1 12.8 - - + -
3099A LEU* 4.5 9.0 - - + -
3144A ASP* 2.9 19.2 + - - +
3192A ILE* 3.9 8.0 - - - +
3500A MG 2.1 33.3 - - - -
3502A ADP 2.6 14.3 + - - -
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Residues in contact with THR3074 (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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3071A GLY* 3.8 8.1 - - - -
3072A LYS 3.4 0.2 - - - -
3073A THR* 1.3 76.1 - - - +
3075A LEU* 1.3 65.0 + - - +
3077A LEU* 3.1 4.6 + - - +
3078A GLN* 3.0 33.6 + - + +
3103A TYR* 3.9 21.8 + - - +
3107A LEU* 3.9 25.9 - - + +
3262A ILE* 3.9 30.5 - - + -
3267A GLY* 4.8 2.5 - - - -
3268A ILE* 5.1 1.6 - - + +
3502A ADP 2.9 31.4 + - - -
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Residues in contact with LEU3075 (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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3042A THR* 4.6 6.7 - - + +
3047A LEU* 4.0 25.8 - - + -
3056A LEU* 5.7 1.1 - - + -
3064A ILE* 3.7 31.2 - - + -
3071A GLY 2.9 20.7 + - - +
3072A LYS* 3.8 3.6 - - - +
3074A THR* 1.3 72.7 - - - +
3076A THR* 1.3 64.4 + - - +
3078A GLN* 3.0 20.1 + - - +
3079A VAL* 3.0 26.4 + - + +
3223A LEU* 4.9 4.3 - - + -
3225A ILE* 4.0 14.8 - - + -
3244A VAL* 4.3 4.5 - - + -
3260A PHE* 3.9 28.5 - - + -
3262A ILE* 5.8 1.1 - - + -
3268A ILE* 4.5 12.1 - - + -
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Residues in contact with THR3076 (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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3064A ILE* 4.1 3.0 - - - +
3072A LYS 3.0 11.3 + - - -
3073A THR 3.1 10.1 - - - +
3075A LEU* 1.3 77.6 - - - +
3077A LEU* 1.3 63.1 + - - +
3079A VAL* 3.2 13.9 + - - +
3080A ILE* 3.1 22.2 + - + +
3092A PHE* 3.5 19.1 - - + -
3142A VAL* 3.3 36.6 - - + +
3190A ILE* 4.0 14.4 - - - +
3192A ILE* 3.4 22.2 - - + +
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Residues in contact with LEU3077 (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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3073A THR* 2.8 37.0 + - + +
3074A THR* 3.6 6.1 - - - +
3076A THR* 1.3 74.3 - - - +
3078A GLN* 1.3 53.5 + - - +
3080A ILE* 3.2 10.9 + - + +
3081A ALA* 2.8 35.2 + - - +
3092A PHE* 4.0 25.8 - - + -
3099A LEU* 4.0 20.2 - - + -
3100A ASP 5.8 0.2 - - - +
3103A TYR* 4.9 6.3 - - + -
3104A ALA* 4.2 22.0 - - + +
3107A LEU* 3.8 23.6 - - + -
3109A VAL* 3.4 18.8 - - + +
3114A LEU* 5.8 3.6 - - + -
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Residues in contact with GLN3078 (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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3042A THR 3.9 12.1 - - - +
3043A GLY* 4.5 7.8 - - - +
3074A THR* 3.0 24.1 + - + +
3075A LEU 3.0 8.0 + - - +
3077A LEU* 1.3 75.5 - - - +
3079A VAL* 1.3 56.4 + - - +
3081A ALA* 3.3 5.5 + - - +
3082A ALA* 3.0 28.6 + - - +
3085A ARG* 4.5 2.7 + - - +
3107A LEU* 3.0 40.7 + - - +
3266A GLU 4.5 1.3 + - - +
3267A GLY* 3.4 7.7 - - - -
3268A ILE* 2.7 53.2 + - + +
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Residues in contact with VAL3079 (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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3040A ILE* 4.5 9.3 - - + +
3041A SER 3.8 20.2 - - - +
3042A THR* 3.6 18.6 + - - +
3056A LEU* 4.6 13.2 - - + -
3075A LEU* 3.0 29.1 + - + +
3076A THR* 3.2 10.5 + - - +
3078A GLN* 1.3 70.2 - - - +
3080A ILE* 1.3 64.3 + - + +
3082A ALA* 3.3 3.2 + - - +
3083A ALA* 2.8 30.1 + - - +
3140A VAL* 4.5 13.0 - - + -
3142A VAL* 5.9 0.2 - - + -
3188A LEU* 4.9 2.2 - - + -
3190A ILE* 3.9 23.6 - - + -
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Residues in contact with ILE3080 (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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3076A THR* 3.1 14.6 + - + +
3077A LEU* 3.4 13.9 - - + +
3079A VAL* 1.3 76.4 - - + +
3081A ALA* 1.3 53.7 + - - +
3083A ALA* 3.0 3.6 + - - +
3084A GLN* 2.8 49.8 + - - +
3090A CYS* 3.8 32.3 - - + -
3091A ALA 4.7 1.6 - - - +
3092A PHE* 3.9 18.4 - - + -
3109A VAL* 4.0 9.9 - - + -
3114A LEU* 3.9 18.2 - - + -
3140A VAL* 4.3 7.2 - - + -
3142A VAL* 3.4 32.3 - - + -
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Residues in contact with ALA3081 (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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3077A LEU 2.8 19.5 + - - +
3078A GLN* 3.5 7.4 - - - +
3080A ILE* 1.3 73.0 - - - +
3082A ALA* 1.3 57.4 + - - +
3084A GLN* 3.4 9.9 + - - +
3085A ARG* 2.9 45.2 + - - +
3107A LEU 3.9 10.8 - - - +
3108A GLY 3.4 32.0 - - - +
3109A VAL* 4.0 3.1 - - + +
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Residues in contact with ALA3082 (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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3040A ILE* 5.4 0.9 - - + -
3041A SER* 4.3 28.0 - - - +
3043A GLY* 5.0 6.1 - - - +
3078A GLN 3.0 16.6 + - - +
3079A VAL* 3.6 5.2 - - - +
3081A ALA* 1.3 75.2 - - - +
3083A ALA* 1.3 62.1 + - - +
3085A ARG* 3.2 36.1 + - - +
3086A GLU* 3.5 16.2 + - - +
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Residues in contact with ALA3083 (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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3040A ILE* 4.4 13.6 - - + +
3079A VAL 2.8 17.4 + - - +
3080A ILE 3.4 4.0 - - - +
3082A ALA* 1.3 74.7 - - - +
3084A GLN* 1.3 59.8 + - - +
3086A GLU* 3.1 23.9 + - - +
3088A LYS* 3.1 31.3 + - + +
3090A CYS* 3.9 4.9 - - - -
3140A VAL* 3.8 28.5 - - + -
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Residues in contact with GLN3084 (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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3080A ILE* 2.8 30.9 + - - +
3081A ALA* 3.7 4.1 - - - +
3083A ALA* 1.3 67.0 - - - +
3085A ARG* 1.3 58.5 + - - +
3086A GLU 2.9 11.0 + - - -
3087A GLY* 2.9 14.7 + - - -
3088A LYS 3.8 18.6 + - - +
3090A CYS* 4.0 11.6 - - - +
3109A VAL* 3.4 9.2 - - - +
3110A ASP* 2.7 57.7 + - + +
3113A ASN* 4.0 7.9 + - - +
3114A LEU* 3.6 24.5 - - - +
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Residues in contact with ARG3085 (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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3078A GLN* 4.5 2.2 + - - +
3081A ALA* 2.9 23.8 + - - +
3082A ALA* 3.2 45.6 - - - +
3084A GLN* 1.3 76.5 - - - +
3086A GLU* 1.3 59.6 + - + +
3087A GLY 3.6 0.6 + - - -
3107A LEU 5.5 0.8 + - - -
3108A GLY* 4.6 7.9 + - - -
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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