Contacts of the strand formed by residues 105 - 109 (chain C) in PDB entry 4GAW
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 MET 105 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C VAL 3.6 0.5 - - - +
55C LEU* 3.3 9.9 - - - +
56C THR* 2.6 53.5 + - + +
57C ALA 3.1 26.0 - - - +
58C ALA* 3.5 8.1 - - - -
60C CYS 3.2 20.6 - - - +
61C GLN* 3.4 37.5 - - + +
89C PRO* 4.1 2.2 - - + -
90C ILE 3.5 16.8 - - - +
91C PRO* 3.9 10.5 - - + -
104C ILE* 1.3 80.4 - - - +
106C LEU* 1.3 68.8 + - - +
107C LEU* 3.7 17.8 + - + -
233C TRP* 4.1 2.5 - - - -
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Residues in contact with LEU 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C VAL* 4.4 6.3 - - + -
53C PHE* 3.5 37.2 - - + -
54C VAL 3.4 5.2 - - - +
55C LEU* 4.1 13.2 - - + -
90C ILE* 2.8 52.4 + - + +
105C MET* 1.3 72.6 - - - +
107C LEU* 1.3 57.9 + - - +
233C TRP* 3.9 8.5 - - + -
234C ILE* 3.8 31.2 - - + -
237C THR* 3.3 25.8 - - - +
238C MET* 3.7 24.2 - - + -
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Residues in contact with LEU 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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33C VAL* 3.8 29.2 - - + -
53C PHE* 2.9 31.2 - - - -
54C VAL* 2.7 39.3 + - + +
56C THR* 4.2 11.0 - - + -
60C CYS 5.5 0.2 - - - +
65C ILE* 4.2 7.4 - - + -
67C VAL* 4.3 3.6 - - + -
86C VAL* 3.7 29.2 - - + -
89C PRO* 3.7 23.8 - - + -
105C MET* 3.7 28.5 + - + -
106C LEU* 1.3 70.1 - - - +
108C GLN* 1.3 62.3 + - - +
109C LEU* 3.8 3.2 + - + +
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Residues in contact with GLN 108 (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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52C ASP* 3.4 13.7 - - + +
53C PHE* 3.9 18.7 - - + -
86C VAL* 3.4 6.6 - - - +
87C LYS* 2.7 64.4 + - - +
88C ARG* 3.3 34.5 + - - +
90C ILE* 4.4 9.6 - - + +
106C LEU 3.8 1.6 + - - -
107C LEU* 1.3 72.7 - - - +
109C LEU* 1.3 62.7 + - - +
241C LEU* 3.7 23.0 + - - -
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Residues in contact with LEU 109 (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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48C LEU* 4.7 2.9 - - + -
51C LYS 3.7 9.4 - - - +
52C ASP* 2.9 34.9 + - - +
53C PHE* 3.9 3.4 - - - +
54C VAL* 4.4 15.0 - - + +
67C VAL* 3.7 30.5 - - + -
69C LEU* 4.7 9.4 - - + -
84C ILE* 4.2 23.1 - - + +
85C PRO 3.7 11.9 - - - +
86C VAL* 4.6 3.6 - - + -
87C LYS* 3.3 13.1 - - - +
107C LEU* 4.4 4.7 - - + +
108C GLN* 1.3 84.9 - - - +
110C GLU* 1.3 61.4 + - - +
111C ARG* 2.8 24.7 + - - +
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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