Contacts of the helix formed by residues 3071 - 3085 (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 GLY3071 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3069D SER 3.4 2.6 - - - -
3070D SER* 1.3 80.5 - - - +
3072D LYS* 1.3 60.5 + - - +
3074D THR* 3.8 0.8 - - - -
3075D LEU* 2.9 34.3 + - - +
3225D ILE* 3.8 7.1 - - - +
3262D ILE* 4.0 14.1 - - - +
3502D ADP 3.0 26.7 + - - -
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Residues in contact with LYS3072 (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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3064D ILE* 4.3 13.6 - - + +
3065D TYR* 3.9 2.5 - - - -
3066D GLY 3.4 20.1 + - - +
3067D PRO 2.7 28.9 + - - -
3070D SER* 3.5 8.3 - - - +
3071D GLY* 1.3 73.6 - - - +
3073D THR* 1.3 62.2 + - - +
3075D LEU* 3.8 2.2 - - - +
3076D THR* 3.0 24.9 + - - -
3192D ILE* 3.6 26.7 - - + +
3193D ASN 3.4 24.9 - - - +
3194D GLN* 5.0 0.9 - - - +
3225D ILE* 3.6 16.2 - - + -
3501D ALF 3.3 24.1 - - - -
3502D ADP 2.7 33.6 + - - +
4217D PHE* 3.8 4.0 - - - -
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Residues in contact with THR3073 (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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3072D LYS* 1.3 73.7 - - - +
3074D THR* 1.3 66.8 + - - +
3076D THR* 3.1 4.4 + - - -
3077D LEU* 2.8 41.2 + - + +
3092D PHE* 4.1 14.4 - - + -
3099D LEU* 4.5 8.5 - - + -
3144D ASP* 2.9 19.4 + - - +
3192D ILE* 3.9 8.7 - - - +
3500D MG 2.1 33.0 - - - -
3502D ADP 2.6 15.2 + - - -
4250D LYS* 5.2 0.4 - - - -
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Residues in contact with THR3074 (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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3071D GLY* 3.8 7.9 - - - -
3072D LYS 3.4 0.2 - - - -
3073D THR* 1.3 76.0 - - - +
3075D LEU* 1.3 65.2 + - - +
3077D LEU* 3.1 4.9 + - - +
3078D GLN* 2.9 34.0 + - + +
3103D TYR* 3.9 22.3 + - - +
3107D LEU* 3.9 22.2 - - + +
3262D ILE* 3.9 30.7 - - + -
3267D GLY* 4.8 6.1 - - - -
3268D ILE* 5.0 1.6 - - + +
3502D ADP 3.0 30.9 + - - -
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Residues in contact with LEU3075 (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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3042D THR* 4.6 7.0 - - + +
3047D LEU* 4.0 26.2 - - + -
3056D LEU* 5.7 1.1 - - + -
3064D ILE* 3.7 30.1 - - + -
3071D GLY 2.9 21.2 + - - +
3072D LYS* 3.8 3.1 - - - +
3074D THR* 1.3 72.9 - - - +
3076D THR* 1.3 64.0 + - - +
3078D GLN* 3.0 21.2 + - - +
3079D VAL* 3.0 26.7 + - + +
3223D LEU* 4.9 5.2 - - + -
3225D ILE* 4.0 14.6 - - + -
3244D VAL* 4.3 4.0 - - + -
3260D PHE* 3.9 28.0 - - + -
3262D ILE* 5.8 1.6 - - + -
3268D ILE* 4.5 12.6 - - + -
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Residues in contact with THR3076 (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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3064D ILE* 4.1 3.4 - - - +
3072D LYS 3.0 12.2 + - - -
3073D THR 3.1 10.5 - - - +
3075D LEU* 1.3 77.4 - - - +
3077D LEU* 1.3 64.4 + - - +
3079D VAL* 3.1 13.5 + - - +
3080D ILE* 3.1 23.0 + - + +
3092D PHE* 3.5 18.2 - - + -
3142D VAL* 3.3 37.2 - - + +
3190D ILE* 4.0 14.8 - - - +
3192D ILE* 3.5 22.5 - - + +
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Residues in contact with LEU3077 (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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3073D THR* 2.8 37.4 + - + +
3074D THR* 3.6 5.6 - - - +
3076D THR* 1.3 73.9 - - + +
3078D GLN* 1.3 53.5 + - - +
3080D ILE* 3.2 10.2 + - + +
3081D ALA* 2.7 35.9 + - - +
3092D PHE* 4.0 26.7 - - + -
3099D LEU* 4.1 20.4 - - + -
3103D TYR* 4.9 6.7 - - + -
3104D ALA* 4.2 21.8 - - + +
3107D LEU* 3.8 24.7 - - + -
3109D VAL* 3.5 18.6 - - + +
3114D LEU* 5.8 2.9 - - + -
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Residues in contact with GLN3078 (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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3042D THR 3.9 12.1 - - - +
3043D GLY* 4.5 7.0 - - - +
3074D THR* 2.9 24.2 + - + +
3075D LEU 3.3 6.7 - - - +
3077D LEU* 1.3 77.0 - - - +
3079D VAL* 1.3 56.9 + - - +
3081D ALA* 3.4 4.5 + - - +
3082D ALA* 3.0 28.2 + - - +
3085D ARG* 4.5 2.5 + - - +
3107D LEU* 3.0 41.5 + - - +
3266D GLU 4.5 1.3 + - - +
3267D GLY* 3.4 7.5 - - - -
3268D ILE* 2.7 53.5 + - + +
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Residues in contact with VAL3079 (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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3040D ILE* 4.4 8.8 - - + +
3041D SER 3.8 20.5 - - - +
3042D THR* 3.6 19.0 + - - +
3056D LEU* 4.5 12.8 - - + -
3075D LEU* 3.0 27.8 + - + +
3076D THR* 3.1 11.4 + - - +
3078D GLN* 1.3 72.0 - - - +
3080D ILE* 1.3 63.8 + - + +
3082D ALA* 3.3 3.0 + - - +
3083D ALA* 2.9 29.1 + - - +
3140D VAL* 4.5 12.3 - - + -
3188D LEU* 4.9 2.2 - - + -
3190D ILE* 3.9 23.8 - - + -
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Residues in contact with ILE3080 (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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3076D THR* 3.1 14.9 + - + +
3077D LEU* 3.4 13.9 - - + +
3079D VAL* 1.3 77.4 - - - +
3081D ALA* 1.3 52.6 + - - +
3083D ALA* 3.0 3.3 + - - +
3084D GLN* 2.8 49.8 + - - +
3090D CYS* 3.8 31.9 - - + -
3091D ALA 4.7 0.9 - - - +
3092D PHE* 3.9 19.1 - - + -
3109D VAL* 4.0 9.2 - - + -
3114D LEU* 3.9 17.0 - - + -
3140D VAL* 4.3 7.0 - - + -
3142D VAL* 3.4 32.1 - - + -
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Residues in contact with ALA3081 (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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3077D LEU 2.7 19.7 + - - +
3078D GLN* 3.5 7.6 - - - +
3080D ILE* 1.3 72.8 - - - +
3082D ALA* 1.3 58.7 + - - +
3084D GLN* 3.3 7.3 + - - +
3085D ARG* 2.9 44.2 + - - +
3107D LEU 3.9 10.8 - - - +
3108D GLY* 3.4 32.2 - - - +
3109D VAL* 4.0 4.7 - - + +
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Residues in contact with ALA3082 (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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3040D ILE* 5.4 1.3 - - + -
3041D SER* 4.2 29.4 - - - +
3043D GLY* 5.0 5.2 - - - +
3078D GLN 3.0 17.2 + - - +
3079D VAL* 3.6 4.5 - - - +
3081D ALA* 1.3 75.8 - - - +
3083D ALA* 1.3 62.9 + - - +
3085D ARG* 3.2 35.0 + - - +
3086D GLU* 3.5 16.4 + - - +
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Residues in contact with ALA3083 (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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3040D ILE* 4.4 13.0 - - + +
3079D VAL 2.9 18.3 + - - +
3080D ILE 3.5 4.3 - - - +
3082D ALA* 1.3 74.5 - - - +
3084D GLN* 1.3 59.8 - - - +
3086D GLU* 3.1 22.8 + - - +
3088D LYS* 3.1 32.2 + - + +
3090D CYS* 4.0 4.7 - - - -
3140D VAL* 3.8 28.0 - - + -
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Residues in contact with GLN3084 (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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3080D ILE* 2.8 30.6 + - - +
3081D ALA* 3.6 4.2 - - - +
3083D ALA* 1.3 67.1 - - - +
3085D ARG* 1.3 58.0 + - - +
3086D GLU 2.9 10.4 + - - -
3087D GLY* 2.9 13.9 + - - -
3088D LYS 3.8 17.9 + - - +
3089D THR* 6.1 0.2 - - - +
3090D CYS* 3.9 11.4 - - - +
3109D VAL* 3.5 9.6 - - - +
3110D ASP* 2.7 57.3 + - + +
3113D ASN* 3.9 7.9 + - - +
3114D LEU* 3.6 24.4 - - - +
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Residues in contact with ARG3085 (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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3078D GLN* 4.5 2.2 + - - +
3081D ALA* 2.9 24.0 + - - +
3082D ALA* 3.2 45.5 - - - +
3083D ALA 3.3 0.2 - - - -
3084D GLN* 1.3 74.8 - - - +
3086D GLU* 1.3 60.3 + - + +
3087D GLY 3.6 1.0 + - - -
3107D LEU 5.5 0.8 + - - -
3108D 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