Contacts of the helix formed by residues 2311 - 2317 (chain D) in PDB entry 6X34
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 CYS2311 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2306D CYS* 5.6 2.2 - - - +
2309D GLN 3.9 1.1 + - - +
2310D SER* 1.3 76.0 - - - +
2312D PRO* 1.3 72.4 - - + +
2313D MET* 4.4 1.8 - - + +
2314D LEU* 3.2 33.9 + - + +
2315D LEU* 3.1 22.2 + - - +
2322D ILE 5.5 0.6 + - - -
2323D GLY 4.5 1.8 + - - -
2325D ASN* 4.2 12.7 - - + +
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Residues in contact with PRO2312 (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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2310D SER 4.2 4.0 - - - +
2311D CYS* 1.3 86.4 - - + +
2313D MET* 1.3 62.6 + - - +
2315D LEU* 3.4 15.0 + - + +
2316D ALA* 3.5 12.3 + - - +
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Residues in contact with MET2313 (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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2311D CYS* 3.3 1.9 - - + +
2312D PRO* 1.3 79.7 - - - +
2314D LEU* 1.3 70.1 + - + +
2316D ALA* 3.7 6.9 + - - +
2317D LYS* 3.6 19.2 + - - +
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Residues in contact with LEU2314 (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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2311D CYS* 3.2 28.3 + - + +
2313D MET* 1.3 85.8 - - + +
2315D LEU* 1.3 59.4 + - - +
2317D LYS* 3.6 4.8 - - + +
2318D GLY* 2.9 29.3 + - - -
2321D ASP* 5.5 2.2 - - - -
2322D ILE* 5.6 8.1 - - + +
2325D ASN* 3.7 21.5 - - + -
2326D PRO* 3.6 19.7 - - + -
2327D CYS* 3.6 34.8 - - - -
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Residues in contact with LEU2315 (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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2310D SER* 6.1 3.4 - - - -
2311D CYS 3.1 15.5 + - - +
2312D PRO* 3.8 8.1 - - + +
2313D MET 3.3 0.6 - - - -
2314D LEU* 1.3 78.6 - - - +
2316D ALA* 1.3 59.4 + - - +
2318D GLY 3.4 17.6 - - - +
2321D ASP* 5.4 12.7 - - + +
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Residues in contact with ALA2316 (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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2312D PRO 3.5 8.7 + - - +
2313D MET* 3.7 8.9 + - - +
2314D LEU 3.3 0.4 - - - -
2315D LEU* 1.3 81.2 - - - +
2317D LYS* 1.3 58.7 + - + +
2318D GLY 3.4 0.6 + - - -
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Residues in contact with LYS2317 (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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2313D MET 3.6 11.6 + - - +
2314D LEU* 3.5 7.8 + - + +
2316D ALA* 1.3 76.9 - - + +
2318D GLY* 1.3 56.7 + - - +
2319D TYR 4.3 0.4 + - - -
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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