Contacts of the strand formed by residues 27 - 30 (chain G) in PDB entry 4QOC
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 LEU 27 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C ALA* 5.0 3.4 - - - +
25G GLU 3.3 6.0 + - - +
26G THR* 1.3 78.5 - - - +
28G VAL* 1.3 64.0 + - - +
47G THR* 4.0 9.9 - - + -
48G TYR* 3.2 7.4 - - - +
49G THR* 3.9 25.1 - - + -
109G VAL* 3.7 0.9 - - - +
110G VAL* 2.9 44.2 + - + +
27I LEU* 3.7 46.9 - - + -
47I THR* 3.9 22.7 - - + -
49I THR* 6.0 0.2 - - + -
110I VAL* 5.9 1.3 - - + -
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Residues in contact with VAL 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G THR* 3.9 17.3 - - + -
27G LEU* 1.3 80.6 - - - +
29G ARG* 1.3 64.8 + - - +
30G PRO* 3.6 4.8 - - + +
47G THR* 3.4 3.7 - - - +
48G TYR* 2.6 44.2 + - + +
50G MET* 4.2 16.8 - - + -
53G VAL* 3.8 27.1 - - + -
107G LEU* 3.9 35.2 - - + -
108G VAL 3.4 6.5 - - - +
109G VAL* 4.0 7.0 - - + -
110G VAL* 3.9 2.9 - - - -
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Residues in contact with ARG 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G VAL* 1.3 72.1 - - - +
30G PRO* 1.3 70.1 - - - +
31G LYS* 3.5 1.0 + - - +
46G ASP* 3.1 25.8 - - - +
47G THR* 2.9 18.7 + - - +
107G LEU* 3.6 1.9 - - - -
108G VAL* 2.7 41.2 + - + +
110G VAL* 3.4 40.4 - - + +
110I VAL* 4.5 18.0 + - - +
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Residues in contact with PRO 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G VAL* 3.6 11.7 - - + +
29G ARG* 1.3 88.3 - - - +
31G LYS* 1.3 66.9 + - - +
32G PRO* 4.8 0.2 - - - +
34G LEU* 3.8 26.2 - - + -
35G LEU* 4.1 17.8 - - + +
38G LEU* 3.6 26.0 - - + -
46G ASP 4.2 5.0 - - - +
48G TYR* 3.7 21.5 - - + -
53G VAL* 4.7 8.3 - - + -
106G ASN 3.6 7.4 - - - +
107G LEU* 4.0 3.4 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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