Contacts of the helix formed by residues 3060 - 3064 (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 LEU3060 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A SO4 3.6 12.3 + - - +
1280A ALA* 4.0 19.5 - - + +
1281A VAL* 4.5 6.5 - - + +
1284A HIS* 3.9 38.4 - - + +
185C SO4 5.6 0.4 - - - +
3058C PRO* 2.6 33.8 + - + +
3059C PRO* 1.3 75.5 - - - +
3061C GLY* 1.3 67.3 + - - +
3062C PRO* 3.3 2.3 - - - +
3063C LEU* 3.1 17.5 + - - +
3114C GLU* 3.6 47.1 - - + +
3115C ASP* 4.0 8.1 - - + +
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Residues in contact with GLY3061 (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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1284A HIS* 3.6 22.1 + - - -
3059C PRO 4.3 0.4 + - - -
3060C LEU* 1.3 72.3 - - - +
3062C PRO* 1.3 70.6 - - - +
3063C LEU 3.1 1.2 + - - -
3064C ARG* 3.2 25.7 + - - +
3114C GLU* 5.1 3.2 + - - -
3287C ARG* 4.2 16.7 - - - +
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Residues in contact with PRO3062 (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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184A SO4 4.3 15.0 - - - +
384C SO4 4.1 11.8 + - - +
3060C LEU 3.8 4.3 - - - +
3061C GLY* 1.3 80.8 - - - +
3063C LEU* 1.3 65.6 + - + +
3064C ARG 3.2 5.0 + - - -
3066C THR* 3.5 9.0 - - - +
3287C ARG* 3.4 25.3 + - - -
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Residues in contact with LEU3063 (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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3057C LYS* 3.7 42.2 - - + +
3058C PRO 3.8 14.1 - - - +
3059C PRO* 3.8 16.9 - - + +
3060C LEU 3.5 11.9 - - - +
3061C GLY 3.1 1.8 + - - -
3062C PRO* 1.3 82.0 - - + +
3064C ARG* 1.3 60.8 + - - +
3066C THR* 2.6 29.4 + - + +
3067C PRO 5.0 1.9 - - - +
3069C GLN* 3.1 37.0 - - + +
3171C ARG* 3.7 10.6 + - - -
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Residues in contact with ARG3064 (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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185C SO4 3.5 11.5 + - - -
3059C PRO 3.8 13.7 + - - +
3061C GLY* 3.2 20.3 + - - +
3062C PRO 3.2 0.8 - - - -
3063C LEU* 1.3 76.4 - - - +
3065C PHE* 1.3 108.1 + - + +
3066C THR* 3.1 3.6 + - - +
3114C GLU* 2.8 39.7 + - - -
3171C ARG* 4.7 2.2 - - - +
3175C TRP* 4.4 11.0 - - + +
3286C LEU 2.8 25.0 + - - -
3287C ARG* 3.1 32.3 + - + +
3289C LYS 2.9 25.6 + - - -
3290C THR 4.2 0.2 - - - -
3291C GLU 4.1 4.0 - - - +
3294C LEU* 3.5 14.3 - - - +
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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