Contacts of the helix formed by residues 3090 - 3102 (chain C) in PDB entry 2DQZ
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 ASP3090 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3089C GLN* 1.3 72.4 - - - +
3091C PRO* 1.3 66.1 - - - +
3092C LYS* 2.9 21.9 + - - +
3093C ALA* 3.1 25.8 + - + +
3094C GLY* 2.8 30.8 + - - -
3145C MET 4.8 0.2 + - - -
3146C VAL* 4.2 5.6 - - + +
3295C LEU* 4.2 6.2 - - - +
3298C THR* 5.3 8.5 - - + +
3299C LEU* 3.5 25.0 - - + +
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Residues in contact with PRO3091 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3086C MET* 5.0 4.7 - - + +
3089C GLN* 3.0 12.0 - - + +
3090C ASP* 1.3 87.0 - - - +
3092C LYS* 1.3 57.1 + - + +
3094C GLY* 3.9 0.6 - - - -
3095C GLN* 3.0 30.3 + - - +
3112C LEU* 4.0 26.2 - - + -
3295C LEU* 4.4 13.2 - - + -
3299C LEU* 5.0 7.0 - - + -
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Residues in contact with LYS3092 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3090C ASP* 2.9 9.4 + - - +
3091C PRO* 1.3 78.6 - - + +
3093C ALA* 1.3 67.5 + - - +
3095C GLN* 3.1 5.6 + - - +
3096C LEU* 3.0 27.1 + - + +
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Residues in contact with ALA3093 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3090C ASP* 3.1 29.2 + - + +
3092C LYS* 1.3 80.1 - - - +
3094C GLY* 1.3 62.1 + - - +
3096C LEU* 3.4 8.1 + - - +
3097C LEU* 3.2 24.4 + - - +
3146C VAL* 4.1 15.0 - - + +
3304C LEU* 6.6 0.4 - - + -
3363C LEU* 5.7 3.9 - - + +
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Residues in contact with GLY3094 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3086C MET* 4.9 9.5 - - - +
3089C GLN* 3.1 28.3 - - - +
3090C ASP 2.8 13.0 + - - -
3091C PRO 4.0 0.7 - - - -
3093C ALA* 1.3 75.0 - - - +
3095C GLN* 1.3 64.2 + - - +
3097C LEU* 3.8 2.8 + - - +
3098C SER* 3.2 23.6 + - - -
3146C VAL* 4.0 7.4 - - - +
3147C GLY* 5.0 2.7 + - - -
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Residues in contact with GLN3095 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3086C MET* 5.0 8.9 - - + +
3091C PRO 3.0 19.5 + - - +
3092C LYS* 3.1 6.5 + - - +
3094C GLY* 1.3 75.3 - - - +
3096C LEU* 1.3 65.6 + - - +
3098C SER* 3.3 6.6 + - - -
3099C GLU* 3.1 43.0 + - + +
3107C ASN* 4.8 7.9 + - - +
3109C PRO* 4.8 13.9 - - - +
3110C LEU 5.0 4.5 + - - +
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Residues in contact with LEU3096 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3092C LYS* 3.0 18.4 + - + +
3093C ALA* 3.7 7.2 - - - +
3094C GLY 3.3 0.2 - - - -
3095C GLN* 1.3 76.9 - - - +
3097C LEU* 1.3 63.2 + - - +
3099C GLU* 3.1 16.1 + - + +
3100C LEU* 3.0 49.4 + - + +
3361C MET* 4.7 10.3 - - + -
3363C LEU* 3.6 25.4 - - + -
3459C MET* 6.5 0.4 - - + -
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Residues in contact with LEU3097 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C COA 4.8 7.6 - - + +
3093C ALA 3.2 14.2 + - - +
3094C GLY 4.2 3.4 - - - +
3096C LEU* 1.3 78.5 - - - +
3098C SER* 1.3 62.8 + - - +
3100C LEU* 3.2 8.4 + - + -
3101C PHE* 3.1 68.0 + - + +
3141C GLY 3.9 20.9 - - - +
3142C GLY* 3.9 7.2 - - - -
3146C VAL* 3.8 24.5 - - + -
3147C GLY* 4.4 9.9 - - - +
3152C TYR* 5.8 0.9 - - - +
3358C LEU* 5.1 0.7 - - + -
3363C LEU* 4.8 20.3 - - + +
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Residues in contact with SER3098 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3086C MET* 6.0 3.6 - - - -
3094C GLY 3.2 17.2 + - - -
3095C GLN* 3.5 7.2 - - - -
3096C LEU 3.2 0.6 - - - -
3097C LEU* 1.3 82.1 - - - +
3099C GLU* 1.3 56.8 + - - +
3102C THR* 3.0 34.7 + - - -
3107C ASN* 3.1 21.9 + - - -
3108C ILE 4.7 4.2 + - - -
3110C LEU* 5.2 6.7 - - - +
3148C ALA* 6.4 0.2 - - - -
3151C THR* 3.2 30.4 + - - +
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Residues in contact with GLU3099 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3095C GLN* 3.1 29.4 + - - +
3096C LEU* 3.1 17.0 + - + +
3098C SER* 1.3 75.8 - - - +
3100C LEU* 1.3 63.0 + - + +
3101C PHE 3.7 0.2 + - - -
3102C THR* 3.8 13.6 - - - +
3107C ASN* 3.3 34.5 + - + +
3482C LYS* 5.1 3.5 + - - -
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Residues in contact with LEU3100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3096C LEU* 3.0 46.6 + - + +
3097C LEU* 3.2 9.4 + - + +
3099C GLU* 1.3 81.2 - - + +
3101C PHE* 1.3 72.7 + - + +
3102C THR 5.2 0.4 - - - -
3357C TRP* 4.4 10.5 - - + -
3358C LEU* 4.2 15.7 - - + +
3361C MET* 4.0 19.3 - - + -
3363C LEU* 4.8 4.9 - - + -
3455C PHE 5.5 0.9 - - - +
3457C SER* 4.0 28.3 - - - +
3473C PHE* 3.6 18.3 - - - -
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Residues in contact with PHE3101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C COA 5.4 3.6 - - - -
3097C LEU* 3.1 39.3 + - + +
3100C LEU* 1.3 93.1 - - + +
3102C THR* 1.3 69.3 + - - +
3103C ASN* 3.4 4.2 + - - +
3141C GLY 5.9 3.8 - - - -
3151C THR* 4.2 7.4 - - + -
3152C TYR* 3.6 33.9 - - + +
3220C GLU* 3.6 21.1 - - - -
3221C SER* 5.8 1.1 - - - -
3358C LEU* 3.5 44.0 - - + -
3468C HIS* 4.1 8.7 - + - -
3469C GLY* 4.2 18.4 - - - -
3472C LEU* 3.8 21.3 - - + +
3473C PHE* 4.4 11.6 - + - -
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Residues in contact with THR3102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3098C SER 3.0 22.6 + - - +
3099C GLU* 3.8 15.4 - - - +
3100C LEU 5.2 0.2 - - - -
3101C PHE* 1.3 79.2 - - - +
3103C ASN* 1.3 57.0 + - - +
3104C ARG* 3.0 39.7 - - - +
3105C LYS 5.0 1.8 - - - +
3107C ASN* 3.7 21.4 + - + +
3151C THR* 3.2 20.6 + - - +
3473C PHE* 3.7 7.3 - - - -
3482C LYS* 3.0 26.8 + - - +
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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