Contacts of the strand formed by residues 104 - 107 (chain C) in PDB entry 4PEI
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 GLY 104 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C LEU* 4.1 12.1 - - - +
103C GLY* 1.3 74.4 - - - -
105C PHE* 1.3 64.7 + - - -
106C VAL 3.5 1.4 + - - -
111C TYR* 3.2 16.9 - - - -
112C TYR* 2.9 34.4 + - - +
336C GLN* 4.4 9.9 - - - -
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Residues in contact with PHE 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C LEU* 4.1 13.2 - - + -
100C LEU* 4.0 2.0 - - - +
104C GLY* 1.3 72.1 - - - -
106C VAL* 1.3 62.0 + - - +
107C CYS 3.6 10.5 - - - +
109C ASN* 4.1 7.2 - - - -
110C MET 3.2 26.0 - - - -
111C TYR* 3.8 22.0 - + + -
269C LEU* 4.1 13.5 - - + -
326C ILE* 3.8 23.6 - - + -
327C ILE 3.4 34.5 - - - -
328C TYR* 3.4 35.0 - + + -
329C ASP* 4.6 7.0 - - + +
333C PHE* 3.6 14.7 - - - -
336C GLN* 4.1 11.6 + - - +
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Residues in contact with VAL 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C THR* 4.4 6.3 - - + +
70C PHE* 3.6 36.2 - - + -
74C TYR* 3.7 7.8 - - - -
86C PHE* 4.0 26.5 - - + -
96C VAL* 4.0 18.2 - - + -
97C LEU* 4.9 1.6 - - + -
100C LEU* 3.7 22.4 - - + -
104C GLY 3.5 2.4 + - - +
105C PHE* 1.3 72.3 - - - +
107C CYS* 1.3 65.8 + - - +
110C MET* 3.0 23.9 + - + +
112C TYR* 4.6 2.9 - - + -
333C PHE* 3.5 20.6 - - + -
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Residues in contact with CYS 107 (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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70C PHE* 3.7 13.9 - - + -
73C TYR* 3.9 24.9 - - - +
74C TYR* 4.1 9.9 - - + +
105C PHE* 3.3 4.7 - - - -
106C VAL* 1.3 79.6 - - - +
108C PHE* 1.3 72.2 + - - +
109C ASN 3.2 0.7 + - - -
110C MET* 3.1 55.9 + - - +
328C TYR* 3.2 22.0 - - - +
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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
------------------------------------------------------------
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