Contacts of the strand formed by residues 2301 - 2306 (chain B) in PDB entry 4D0N
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 GLY2301 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2294B GLU* 4.3 0.2 - - - -
2295B VAL* 3.5 18.4 + - - -
2298B GLU* 3.0 11.4 + - - +
2300B LYS* 1.3 78.4 - - - +
2302B LEU* 1.3 62.6 + - - -
2317B VAL 3.4 8.1 - - - -
2318B HIS* 3.7 18.4 + - - -
2325B ARG* 3.0 25.7 + - - -
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Residues in contact with LEU2302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2292B VAL* 3.3 32.8 - - + -
2293B ARG 3.3 17.3 - - - +
2295B VAL* 3.1 12.5 - - - +
2301B GLY* 1.3 76.3 - - - +
2303B PHE* 1.3 65.8 + - - +
2304B LEU* 4.4 3.6 - - + -
2316B GLU* 3.4 4.3 - - - +
2317B VAL* 2.8 58.4 + - + +
2325B ARG* 4.2 12.6 - - + +
2328B TRP* 4.2 22.4 - - + -
2329B ILE* 3.5 19.1 - - + -
2332B ILE* 4.6 10.8 - - + -
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Residues in contact with PHE2303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2291B ILE 3.7 0.3 - - - +
2292B VAL* 3.5 3.5 - - - -
2293B ARG* 2.6 46.8 + - + +
2294B GLU 4.1 11.4 - - - -
2295B VAL* 3.7 32.5 - - + -
2296B ALA 5.1 1.6 - - - -
2302B LEU* 1.3 79.8 - - - +
2304B LEU* 1.3 61.3 + - - +
2305B ILE* 4.2 3.6 - - + -
2314B MET* 3.6 49.6 - - + -
2315B VAL 3.5 0.7 - - - -
2316B GLU* 3.6 42.4 - - + -
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Residues in contact with LEU2304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2263B LEU* 3.6 25.8 - - + -
2265B PHE* 4.2 19.1 - - + -
2285B ILE* 4.7 7.6 - - + -
2290B LEU* 4.1 24.0 - - + -
2291B ILE 3.4 1.8 - - - -
2292B VAL* 4.0 29.4 - - + -
2302B LEU* 4.4 5.4 - - + -
2303B PHE* 1.3 79.8 - - - +
2305B ILE* 1.3 61.6 + - - +
2306B SER* 4.1 0.8 + - - -
2313B GLU 3.4 2.8 - - - +
2314B MET* 3.2 3.1 - - - -
2315B VAL* 2.8 51.1 + - + +
2317B VAL* 4.5 9.9 - - + -
2332B ILE* 4.3 13.7 - - + -
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Residues in contact with ILE2305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2289B LYS 3.9 0.2 - - - +
2290B LEU* 3.5 4.7 - - - +
2291B ILE* 2.9 49.4 + - + +
2293B ARG* 4.2 35.4 - - + +
2303B PHE* 4.8 3.6 - - + -
2304B LEU* 1.3 76.0 - - - +
2306B SER* 1.3 60.1 + - - +
2307B MET* 3.2 33.2 + - - +
2312B PRO* 4.0 15.5 - - + +
2313B GLU 3.5 4.9 - - - +
2314B MET* 3.9 29.4 - - + -
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Residues in contact with SER2306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2221B LYS* 4.3 16.9 - - - +
2285B ILE* 3.6 27.9 - - - +
2286B SER 5.0 0.8 + - - -
2289B LYS 4.7 1.8 - - - -
2290B LEU* 3.8 7.5 - - - +
2304B LEU 5.3 0.2 + - - -
2305B ILE* 1.3 67.6 - - - +
2307B MET* 1.3 61.9 + - - +
2308B GLY 3.2 3.1 + - - -
2309B MET* 3.7 22.3 - - - +
2312B PRO* 3.1 22.8 - - - +
2313B GLU* 2.9 19.4 + - - +
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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